Use "wiring" (not "stk500v2") avrdude protocol for uploads to Mega 2560.

It performs the auto-reset in avrdude.  Otherwise, some uploads seem to fail (possibly because it takes too long to launch avrdude from the IDE, so there's too much of a delay between the auto-reset done by the IDE and the upload).

http://code.google.com/p/arduino/issues/detail?id=806

Author: damellis

hardware/arduino/boards.txt

@@ -106,7 +106,7 @@ nano.build.variant=eightanaloginputs
 
 mega2560.name=Arduino Mega 2560 or Mega ADK
 
-mega2560.upload.protocol=stk500v2
+mega2560.upload.protocol=wiring
 mega2560.upload.maximum_size=258048
 mega2560.upload.speed=115200