Just to make certain I understand: When you upload from the command-line, does the verify work? Or do you have avrdude skip the verify?
Does verify work from the IDE if you enable verbose output?
The bootloader is the STK500v2 at 115200 with a 16mhz clock.I verified that avrdude will connect to the bootloader (avrdude -pm2561 -cstk500v2 -b115200 -P/dev/ttyUSB1)avrdude -pm2561 -b57600 -cstk500v2 -P/dev/ttyUSB1 -U flash:w:Blink.cpp.hex
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