I'm having the same problem. I received my Mega2560 2 days ago. Until this afternoon, everything was working fine. Suddenly the same code that was uploading wouldn't upload any longer. I hadn't changed anything. I've read a bunch of threads, tried changing the AVRDUDE.EXE to an older version that someone posted on a different site, modified the boards.txt file to "wiring" as indicated here, tried using the ISP programmer vs the ISP mkII programmer and vice-versa- nothing works. I can't upload any programs. They all do this same thing. Very strange since it was working just fine earlier...
Here's an output from my verbose upload after I reverted everything back to the original EXCEPT I kept the "wiring" setting in the boards.txt:
Binary sketch size: 3,496 bytes (of a 258,048 byte maximum)
C:\Users\Cameron\Desktop\arduino-1.0.1\hardware/tools/avr/bin/avrdude -CC:\Users\Cameron\Desktop\arduino-1.0.1\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega2560 -cwiring -P\.\COM5 -b115200 -D -Uflash:w:C:\Users\Cameron\AppData\Local\Temp\build1215771844599652454.tmp\MegaTEST.cpp.hex:i
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 Wunsch
System wide configuration file is "C:\Users\Cameron\Desktop\arduino-1.0.1\hardware/tools/avr/etc/avrdude.conf"
Using Port : \.\COM5
Using Programmer : wiring
Overriding Baud Rate : 115200
avrdude: wiring_open(): releasing DTR/RTS
avrdude: wiring_open(): asserting DTR/RTS
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
Any thoughts?
Thanks,
Cameron