I am sure this came up before, but google didn't help me much in this case
I get the following log when trying to burn the Leonardo bootloader on a standalone sytem.
C:\Program Files (x86)\Arduino\hardware/tools/avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega32u4 -cstk500v2 -Pusb -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m
avrdude: Version 5.11, compiled on Sep 2 2011 at 19:38:36
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg WunschSystem 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: 000200012345
avrdude: usbdev_open(): using read endpoint 0x83
avrdude: Sent: . [01]
avrdude: Recv: . [01] . [00] . [0a] A [41] V [56] R [52] I [49] S [53] P [50] _ [5f] M [4d] K [4b] 2 [32]
avrdude: stk500v2_getsync(): found AVRISP mkII programmer
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 10 8 0 no 1024 8 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
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
avrdude: Sent: . [03] . [90]
avrdude: Recv: . [03] . [00] . [00]
avrdude: Sent: . [03] . [91]
avrdude: Recv: . [03] . [00] . [01]
avrdude: Sent: . [03] . [92]
avrdude: Recv: . [03] . [00] . [11]
Hardware Version: 0
Firmware Version Master : 1.17
avrdude: Sent: . [03] . [94]
avrdude: Recv: . [03] . [00] ! [21]
Vtarget : 3.3 V
avrdude: Sent: . [03] . [98]
avrdude: Recv: . [03] . [00] . [06]
SCK period : 8.00 usavrdude: Sent: . [10] . [c8] d [64] . [19] [20] . [00] S [53] . [03] . [ac] S [53] . [00] . [00]
avrdude: Recv: . [10] . [c0]
avrdude: stk500v2_command(): command failed
avrdude: Sent: . [03] . [a1]
avrdude: Recv: . [03] . [00] . [00]
avrdude: stk500v2_program_enable(): bad AVRISPmkII connection status: Unknown status 0x00
avrdude: initialization failed, rc=-1
Double check connections and try again, or use -F to override
this check.avrdude: Sent: . [11] . [01] . [01]
avrdude: Recv: . [11] . [00]avrdude done. Thank you.
Trying the same on a working Leonardo and comparing logs they seem to differ on
avrdude: Sent: . [10] . [c8] d [64] . [19] [20] . [00] S [53] . [03] . [ac] S [53] . [00] . [00]
avrdude: Recv: . [10] . [c0]Vs
avrdude: Sent: . [10] . [c8] d [64] . [19] [20] . [00] S [53] . [03] . [ac] S [53] . [00] . [00]
avrdude: Recv: . [10] . [00]
Any ideas?