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.