Can ONLY program sketch when holding shift key

Hi,

I have a Atmel AVRISP MK2 using libUSB 1.2.6.0 drivers (USB\VID_03EB&PID_2104)
Running windows 7 64, Core2 quad , 8GB ram.
Arduino 1.6.4

If i upload a sketch inside Arduino it ONLY works if i hold the shift key down to show debug messages.
If i don't hold the shift key arduino just locks up (no flashing lights on AVRISP at all) Avrdude also hangs in the background and the task needs to be killed)
But if i hold the shift key then programming a sketch works 100% fine

If i upload a bootloader it never works, even with the shift key, i can see from the Arduino log that it's writing all the fuse bits correctly but when it gets to the actual bootloader firmware it cant see the usb device any more.

If i copy paste the arduino avrdude command lines being run and instead run them myself in a command window they always work 100% fine.

The only thing i can think of is that Arduino is trying to run consecutive calls to avrdude/avrispmk2 too quickly after the previous attempt and something is not ready.
When holding shift the timing will be a little slower because of the extra time needed to process/print the debug messages to the UI and maybe this fixes the issue sometimes.

I do notice a single USB windows sound during attempts to flash a bootloader in arduino. Which could indicate that the AVRISP is rebooting or something after the previous connection and arduino maybe trying to talk to it during this time?

Below is a log from Arduino when it tries to flash a bootloader

Any ideas?

C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -cstk500v2 -Pusb -e -Ulock:w:0x3F:m -Uefuse:w:0x05:m -Uhfuse:w:0xDA:m -Ulfuse:w:0xFF:m 

avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"

         Using Port                    : usb
         Using Programmer              : stk500v2
avrdude: usbdev_open(): Found AVRISP mkII, serno: 000200215490
         AVR Part                      : ATmega328P
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PC2
         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  3600  3600 0xff 0xff
           flash         65     6   128    0 yes     32768  128    256  4500  4500 0xff 0xff
           lfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
           lock           0     0     0    0 no          1    0      0  4500  4500 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 : STK500V2
         Description     : Atmel STK500 Version 2.x firmware
         Programmer Model: AVRISP mkII
         Hardware Version: 1
         Firmware Version Master : 1.23
         Vtarget         : 4.6 V
         SCK period      : 8.00 us

avrdude: AVR device initialized and ready to accept instructions

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

avrdude: Device signature = 0x1e950f
avrdude: erasing chip
avrdude: reading input file "0x3F"
avrdude: writing lock (1 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x3F:
avrdude: load data lock data from input file 0x3F:
avrdude: input file 0x3F contains 1 bytes
avrdude: reading on-chip lock data:

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

avrdude: verifying ...
avrdude: 1 bytes of lock verified
avrdude: reading input file "0x05"
avrdude: writing efuse (1 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of efuse written
avrdude: verifying efuse memory against 0x05:
avrdude: load data efuse data from input file 0x05:
avrdude: input file 0x05 contains 1 bytes
avrdude: reading on-chip efuse data:

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

avrdude: verifying ...
avrdude: 1 bytes of efuse verified
avrdude: reading input file "0xDA"
avrdude: writing hfuse (1 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of hfuse written
avrdude: verifying hfuse memory against 0xDA:
avrdude: load data hfuse data from input file 0xDA:
avrdude: input file 0xDA contains 1 bytes
avrdude: reading on-chip hfuse data:

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

avrdude: verifying ...
avrdude: 1 bytes of hfuse verified
avrdude: reading input file "0xFF"
avrdude: writing lfuse (1 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of lfuse written
avrdude: verifying lfuse memory against 0xFF:
avrdude: load data lfuse data from input file 0xFF:
avrdude: input file 0xFF contains 1 bytes
avrdude: reading on-chip lfuse data:

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

avrdude: verifying ...
avrdude: 1 bytes of lfuse verified

avrdude done.  Thank you.

C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -cstk500v2 -Pusb -Uflash:w:C:\Program Files (x86)\Arduino\hardware\arduino\avr/bootloaders/atmega/ATmegaBOOT_168_atmega328.hex:i -Ulock:w:0x0F:m 

avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"

         Using Port                    : usb
         Using Programmer              : stk500v2
avrdude: usbdev_open(): did not find any USB device "usb"
Error while burning bootloader.

it ONLY works if i hold the shift key down to show debug messages.

"Shift" hasn't caused the "show debug message" behavior in a long time (since 1.0?)
In newer versions, it causes "upload using programmer" instead. this has implications:

  1. this won't work if you don't have the programmer attached.
  2. It erases the bootloader, so subsequent attempts at normal uploads won't work.

There's a well-known problem with some programmers (notably Dragon) where after an avrdude command, the USB interface resets/re-enumerates. If a subsequent avrdude command is issued before windows finishes the USB enumeration, it will fail.

avrdude -patmega328p -Uflash:w:C:/.../bootloaders/atmega/ATmegaBOOT_168_atmega328.hex:i

Is there a reason you're not using the Uno bootloader (Optiboot)?