I' used my USBASP adapter in ISP pins of board, using Arduino 1.0.3 to program 2560 chip.
At the end of programming with Arduino I got this message:
Binary sketch size: 203.542 bytes (of a 258.048 byte maximum)
avrdude: verification error, first mismatch at byte 0x0000
0x0c != 0xff
avrdude: verification error; content mismatch
The USBasp programmers do not properly support the large memory space of the mega2560. However, others have just ignored the verification errors and said it still works.