Try doing this:
avr-objdump -j .sec1 -d -m avr5 stk500boot_v2_mega2560.hex > somefile.txt
That disassembles it. Then do it to the code you downloaded from the board. Then do a file compare (eg. diff).
Try doing this:
avr-objdump -j .sec1 -d -m avr5 stk500boot_v2_mega2560.hex > somefile.txt
That disassembles it. Then do it to the code you downloaded from the board. Then do a file compare (eg. diff).