Grumpy_Mike:
probably not reseting pins to input mode.
No that happens automatically as a result of the reset pin being hit. It is a hardware thing.
I'm not so sure, the Uno/Optiboot 'features' and the new 8u2 usb converter chip sure made for a rather rocky introduction to the latest board offerings from Arduino, with more bugs then any other new board offerings I can recall. And also requiring two IDE releases in very short order.
In hind site they would probably been better off just introducing the 8u2 feature and put off changing from their more proven bootloader code. That or they need a better beta process before rushing new boards to market.
My money 2 cents is that this symptom uncovered in this posting will be at least related to the new bootloader if not directly caused by it. No proof, just shooting from the hip. 