Hello guys, I am experiencing the same situation with 2 out of 3 my Mega's2560.
the interesting point is that 2 of these boards that have a proble are mega 2560 and third one which runs just fine is mega 2560 R3.
the simptoms are - during (second after connecting the ARD to usb) uploading the board freezeng tx rx leds blin once, IDE freezeng, in task manager I see avrdude.exe stocked .
very first time it usially works OK.
only way to exit - to kill avrdude .
it does not matter which file I try to upload, which PC + OS I use ( I checked 3 PC with XP and 7 ).
seems to me - it is disign flaw in mega2560 - something is really wrong with booloader.