I have a slightly later version, although that shouldn't make much difference.
I seem to be able to upload the blink sketch OK:
Reading SD card ...
HEX files in root directory:
BLINKC~1.HEX : 4616 bytes. Created: 2012-08-05 09:28:00. Modified: 2012-08-05 09:28:00
--------- Starting ---------
Attempting to enter programming mode ...
Entered programming mode OK.
Signature = 0x1E 0x98 0x01
Processor = ATmega2560
Flash memory size = 262144 bytes.
LFuse = 0xFF
HFuse = 0xD8
EFuse = 0xFD
Lock byte = 0xEF
Clock calibration = 0x5D
Actions:
[E] erase flash
[F] modify fuses
[L] list directory
[R] read from flash (save to disk)
[V] verify flash (compare to disk)
[W] write to flash (read from disk)
Enter action:
W
Choose disk file [ ] ...
BLINKC~1.HEX
Processing file: BLINKC~1.HEX
Checking file ...
###
Lowest address = 0x0
Highest address = 0x65F
Bytes to write = 1632
No bootloader.
Suggest making high fuse = 0xD9
Attempting to enter programming mode ...
Entered programming mode OK.
Processing file: BLINKC~1.HEX
Erasing chip ...
Writing flash ...
#######
Written.
Processing file: BLINKC~1.HEX
Verifying flash ...
######
No errors found.
No bootloader.
Setting high fuse = 0xD9
Done.
What is your hardware exactly? I am using the Mega2560 board. Are you using that? If not, what speed are you running the processor at (eg. what crystal)?
Judging by the errors, the data is not uploading correctly.
You could try slowing it down. Find this line in the sketch:
// control speed of programming
const byte BB_DELAY_MICROSECONDS = 4;
Try making the 4 larger (eg. 8) and see if that helps.
Latest version of GitHub: