Sorry if this is seen as a repost, but after wandering around it seemed that this section was more appropriate.
Can you reproduce? (we can, each time, using any program, even 'blink')
We finally found that simply taking a 4.7k resistor from the board 5V to pin 7 causes the problem. On original UNO, this works.Can you reproduce? (we can, each time, using any program, even 'blink')
If you take the AVR out of one of the new and misbehaving boards, and put it in a Rev1 board, does it start behaving?
I tried that. Swapping AVR from a R1 UNO to R2 UNO does not change behavior. [...]
a little confused here - can you just clarify: if you swap the 328p chips over, the R1 works (is not disrupted by a pullup on D7) while the R2 stops working with the pullup present?
is the 328p getting good power? that is a solid 5v, preferably monitored with a scope for any spikes. remembering that the power comes via a FET that is wired up in an arrangement that has been questioned in the past.