Did I fry my DUE by powering it from a external source and USB at the same time? If so, why? I guess I just fried my second DUE in a week. The first I didn't really see what happened, but I couldn't upload any sketches, even if the computer could recognize it, and the SAM would get really hot.

Now, I had it powered by a 12V External supply, through a regulator bringing it down to 9V, and in the exact moment I plugged the USB, with power still on, I got a lot of smoke, smelling of fried electronics :p. Afterwards, I have the same symptoms as I had in the other boards: Green and orange LEDs on, chip very hot, computer recognizing it as a Arduino DUE but not being able to upload any sketches.

What just happened?
If it was the same sketch involved in the destruction of both it may be a good idea to check to make sure the sketch that is involved as well to make sure there are no logical shorts to ground or other pins. Rugged-Circuits has a list of some common ways the Arduino can get shorted. It is showing the Uno but I am sure all similar rules apply with the exception of total power requirements and other differences between the boards.