Yikes! Invalid device signature (0xffffff/0x000000/0xff0000

Hi and thanks for opening this forumpost.
I have two unresponsive arduino micro's that both do not show up in USB ports when I connect the usb cable. I've tried to burn bootloader onto them using another arduino micro that does show up in the usb ports. With either troublesome arduino wired up it can't seem to read the device signature. It looks like to me it reads a different device signature at every attempt.
I've set programmer to "Arduino as ISP (ATmega32U4)"
I've set the board to "Arduino/Genuino Micro"
I've followed the wiring and it looks something like this, (Arduino Bootloader Wiring Diagram) but imagine both programmer and receiver being arduino micro's

  • Also i've tried to add a 22 MFD capacitor between GND and RST

I've tried around 10 different similar posts and my head is spinning but they did not really reflect my exact situation almost every time.

I've triple checked cable connection to see if anything didn't actually connect.
Once, it seemed to work after many attempts but the board still doesn't show up in the ports list. After attempting again get the same results:

avrdude: Version 6.3-20190619
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2014 Joerg Wunsch

         System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
         User configuration file is "/Users/jorickbronius/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/cu.usbmodem14201
         Using Programmer              : arduino
         Overriding Baud Rate          : 19200
         AVR Part                      : ATmega32U4
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
           flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : Arduino
         Description     : Arduino
         Hardware Version: 2
         Firmware Version: 1.18
         Topcard         : Unknown
         Vtarget         : 0.0 V
         Varef           : 0.0 V
         Oscillator      : Off
         SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xff0000
avrdude: Expected signature for ATmega32U4 is 1E 95 87
         Double check chip, or use -F to override this check.

avrdude done.  Thank you.


I am quite a beginner at this and spent already many hours getting seemingly absolutely no where. Help is muuuch appreciated. :sweat_smile:

Edit: During these attempts I've had the ArduinoISP example loaded onto the responsive master Micro. I did not however changed the wiring according to the Micro Pinout

When you have the Micro plugged in, double short the RESET to GND with a wire, a port should then show up.

Just to make sure, have you uploaded 'ArduinoISP' onto the functioning micro ?
(there is a lot of information in the comments of that sketch btw)
But i suspect that you just connected it to pins 10 - 13 the same way as you would do on an UNO, but the pinout is different.
SCLK is pin 9 on a Micro (to 13 on an UNO)
MOSI on pin 10 and MISO on pin 11,
That means that the reset pin will also need to moved.
You can try use wiring for software SPI as well, but i suggest you try using hwSPI first.

Hey!
Thanks, for your suggestion! I followed it, but no dice.

Hi and thanks a bunch for your response!

Right, I forgot to add that to the list of "have tried". Sorry, too many steps to cover/remember to note.

You are correct, that is exactly what I did.

So following your suggestion I connected the slave's ICSP/SPI pins:

  • MISO to the masters pin 11
  • SCK to 9
  • 5V to 5V
  • MOSI to 10
  • GND to GND
    and currently I have the ICSP/SPI reset header pin connected to 12. Does that mean I have to change it in the ArduinoISP example to 12 too in line 73?
    In fact, does that mean I have to declare for all the changed pins in the code? And if so, on which lines in the code? I can't find it, unless I have to do the "USE_OLD_STYLE_WIRING" line and then change all pins accordingly?

Because when I try to burn bootloader using the "Arduino as programmer (ATmega32U4)" as selected programmer with the ArduinoISP example as is, I still get the following

error message:

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem142101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem142101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.

avrdude done. Thank you.

However when doublechecking all wiring and changing all pins in code accordingly via the USE_OLD_STYLE_WIRING way, I end up with the following

error message

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem142101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem142101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xfffe00
avrdude: Expected signature for ATmega32U4 is 1E 95 87
Double check chip, or use -F to override this check.

avrdude done. Thank you.

error message when trying burn bootloader on second unresponsive arduino

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem142101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem142101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x0000ff
avrdude: Expected signature for ATmega32U4 is 1E 95 87
Double check chip, or use -F to override this check.

avrdude done. Thank you.

All these attempts are without the capacitor, though. Is it neccesary?
I'm in a dark forest :evergreen_tree: :deciduous_tree: :evergreen_tree: and can't find the bug :spider:

Yes.

Eh, no. What are the SPI pins is part of the boards definitions, what needs to be changed is just the reset pin.
Either you specify OLD_STYLE_WIRING and use pins 10-13 as on an UNO or you connect them to the SPI pins as defined for the board.

Not sure either.

So, I tried this, with RESET on 10

and checked all cabling twice. The following came up:

Error message with OLD_STYLE_WIRING

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem141101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem141101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x0007ff
avrdude: Expected signature for ATmega32U4 is 1E 95 87
Double check chip, or use -F to override this check.

avrdude done. Thank you.

When I do this, with RESET connected to the pin labeled RS and check all wiring again, I still get the following problem:

Summary

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem141101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem141101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xfff800
avrdude: Expected signature for ATmega32U4 is 1E 95 87
Double check chip, or use -F to override this check.

avrdude done. Thank you.

There's no burnt out components on the boards.

I did get confused at first, though. Because the pinout on the page you linked shows scrambled numbers in grey going up to 42, but they do not at all coincide with the numbers next to the actual pins on the board(like 12 is 11 and 26 is 12). What are these referring to? Which numbers are corresponding to the ones declared in the code? Must be the grey ones, right? Since they show 10 next to MOSI etc.

Now I move the reset to the pin labeled 11~ on the board, which is labeled 12 in grey in the Pinout overview, and changing line 73's reset defining to 12. I get this:

Error after following grey labeling

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem141101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem141101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.

avrdude done. Thank you.

However, trying the same thing on the 2nd problematic board, results in:

Error after following grey labeling, 2nd board

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem141101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem141101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x00ffff
avrdude: Expected signature for ATmega32U4 is 1E 95 87
Double check chip, or use -F to override this check.

avrdude done. Thank you.

:brick: :brick: :brick: :brick:

I am continuing this journey here, since I am no longer sure these boards are just bricked. I will still look into this thread when updated, might any of you have another idea regarding the bootloader situation, and I will update also here when a conclusion has shown itself either here or on the other side.

Many thanks for your input!

this might be a better overview of the pin connections.
And basically you can use any pin you like for 'reset'
I see now how it may be confusing, since actually the SPI pins are not normal GPIO pins at all (I hadn't seen that before, due to the rotation of the picture of the board)

It is a little confusing for me as well, i think they respond to the pin numbers of the actual chip that is on the board.
I would try to actually do it myself now, but i am lacking time little at the moment.

Have you changed the programmer type to use 'Arduino as ISP' instead of the 32u4 version ?

What makes them seem to abnormal to you? For me everything on this board is every bit as alien as the SPI pins :joy:

I also had this thought at some point, but putting the chip pinout and the board pinout next to each other I see that 29 on the chip is digital pin 9, 5v pin and the 3.3v pin. So that got my head spinning more, however 9, 10 & 11 do correspond with the SCK, MOSI and MISO respectively.
So when I put the reset back at chip pin 13 and tell the code to look for it there. I still get these same looking error with both boards:

Faulty board 1

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem142101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem142101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0xffffff (probably .avr8x_mega)
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.

avrdude done. Thank you.

Faulty board 2

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -carduino -P/dev/cu.usbmodem142101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem142101
     Using Programmer              : arduino
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : Arduino
     Description     : Arduino
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.

avrdude done. Thank you.

Following this suggestion I the console gives me something I'm getting familiar with:

Faulty board 1

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -cstk500v1 -P/dev/cu.usbmodem142101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem142101
     Using Programmer              : stk500v1
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : STK500
     Description     : Atmel STK500 Version 1.x firmware
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000 (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.

avrdude done. Thank you.

Faulty board 2

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Micro"

/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -cstk500v1 -P/dev/cu.usbmodem142101 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf"
     User configuration file is "/Users/jorickbronius/.avrduderc"
     User configuration file does not exist or is not a regular file, skipping

     Using Port                    : /dev/cu.usbmodem142101
     Using Programmer              : stk500v1
     Overriding Baud Rate          : 19200
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : STK500
     Description     : Atmel STK500 Version 1.x firmware
     Hardware Version: 2
     Firmware Version: 1.18
     Topcard         : Unknown
     Vtarget         : 0.0 V
     Varef           : 0.0 V
     Oscillator      : Off
     SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Error while burning bootloader.
Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x0000ff
avrdude: Expected signature for ATmega32U4 is 1E 95 87
Double check chip, or use -F to override this check.

avrdude done. Thank you.

I have the same problem also. But I am using a bare atmega32u4. Can't seem to fix it.