retrolefty:
Well the Uno in rev2 and the present rev3 did add a 1K ohm pull-down resistor on the DTR output pin from the 16U2 chip that the older arduino 2009 board did not use on the FTDI DTR output. I wonder if that pull-down resistor keeps the 328p reset pin low long enough after initial power-up to cause a true pin1 external reset condition and thus activation the bootloader wait period to be active?
Just to be clear, the tests I did were not on Uno boards. I did my testing on a clone board modeled after the original issue Uno, but with FT232RL instead of the 8U2 for USB-serial. The 1K pull-down you mention is not on my board, but it does have the clamping diode on the RESET line that was added to later Uno's.
Jim