For those of you Mac users who also have trouble uploading your programs to the Mega 2560 because of timeout problems... maybe I have a fix for you!
Download the Wiring app (Download \ Wiring) and copy the two files
../Wiring.app/Contents/Resources/Java/tools/avr/bin/avrdude
and
../Wiring.app/Contents/Resources/Java/tools/avr/bin/avrdude.conf
into
../Arduino.app/Contents/Resources/Java/hardware/tools/avr/bin/
after renaming the avrdude utility inside there into avrdude_old or something like that.
Now start the Arduino app again. Everything should work perfect now!
The german guys here also can check out my blog post http://www.p0lar.is/?q=node/6.
Enjoy... 