foubarre:
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?
this might suggest a problem in the area of the USB controller the UNO uses, where the presence of the pullup affects how the bootloader responds to incoming serial traffic from the 8U2. but this still depends on the bootloader "caring" that a pullup is present.
another thing to check on - 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.