afremont:
Interesting. I looked at the datasheet for the regulator and it does indeed have an internal protection diode connecting Vout to Vin. It is capable of handling a 50A surge which is far in excess of what might be encountered in normal cycling of the device. In case the Vin is shorted to ground and Vout contains more than about 50uF of capacitance could this limit be exceeded requiring another external diode. I think reports of connecting a truly regulated 5V supply to the +5V pin causing damage are highly suspect.
It is a puzzle, but a few posters have reported their boards damaged doing it soon after the rev3 boards were released, but who knows the true root cause?
It just got more interesting when out of the blue (or maybe based on analysis of returned damaged boards?) the Arduino folks added the 5V pin warning on several of their current board offerings.
Lefty