I am having the SAME issue onthesamehardware, although I have noled functionality. Mega R3. I blamed me though, and that i had ruined the hardware somehow. i base that theory on the 500 ma draw, and the fact the atmega chip was getting warm. could you verify that your chip is not getting warm? I think my issue is different, but if yours is hot too, maybe its less my fault.
i am running arduino IDE 1.0 on an ubuntu machine, been running the 1204 pre for some time.