I have now encountered a 4'th mega r3 that is encountering usb communication difficulties - and I'm about 99.9% certain I have NEVER plugged this one into two power supplies - only the usb power. The trouble began with seeing 'garble' when the mega was reset, my sketch should print 'status' to the serial port upon reset and 'sometimes' it was garbled. Huh...Maybe just trash on the line I thought. But then, when I pushed the reset button it began not writing to the serial port at all sometimes. I'd have to close the arduino ide's comm window, unplug/replug the usb cable back in, reopen the comm window, and then upon reset could get it to speak on an intermittent basis. Sometimes it would stop talking after 5 resets, sometimes after 3 resets, one one round I got all the way to 24 resets before it stopped talking.
At that point I moved from the macintosh over to the pc and found the exact same symptoms (ocasional garble, and dying after some low number of resets).
At that point I grabbed a mega rev2, loaded the exact same software onto it, and it works perfectly.
I went back to the mega rev3, reloaded the software - and it's intermittent, and it got worse the longer it was on. It looks to me like I'm catching the beginnings of a usb controller chip failure.
So, it's beginning to look like a bad batch of mega rev 3, or a design flaw, one or the other, to me. I'll be working on the mega rev2 all day and tomorrow, and will keep it continuously powered up and will report back later.