afremont:
I was wondering if that might be the issue. I didn't look at the datasheet for the regulator being used now, but with something like a 7805 you're not supposed to allow the output pin to be higher than the input. A diode is often used to route voltage back to the input pin. I would have hoped that a modern part would automatically include this trivial feature to protect the regulator. Applying +5V to Vin and the +5V pin should eliminate the problem by prevent the reverse bias of the regulator.I have seen quite a few recommendations to do what I suggested, but hadn't read yet of anyone experiencing any problem. I didn't search for it though.
And the thing about it that puzzles me is that when one is powering a board with just USB power the on-board regulator also then has +5vdc applied to it's output with nothing on it's input, so what is the difference in that case as when one applies a regulated +5vdc to the 5V pin? The only think I can think of is that there is some current limiting when on USB power via the 500ma thermofuse, so maybe that limits a possible peak current spike/path going backwards through the regulator? Who knows, but the diode addition sounds like cheap insurance if one is going to power via the 5V pin.
Lefty