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.