I can confirm this problem, as I too just fried the usb ports on three mega's, doing the exact same thing. And since it doesn't happen immediately upon plugging in both power supplies you get fooled into thinking you must have done something else wrong, thus you plug in another mega, it works, for awhile, then stops talking, and about this time you've got suspicions, but you're obligated to plug in and kill a third one to confirm it....ouch is right.
Here's the link to my post for what it's worth.
http://arduino.cc/forum/index.php/topic,98728.0.html
Does anybody involved in the mega r3's design have any thoughts on what's going on here?