this is probably NOT the problem, but on the minutest chance it is... i've a feeling i read somewhere about the UNO's being shipped with an alternative bootloader, called "optiboot". this new bootloader is 1/4 the size (512 bytes) of the original (2k). i don't know, off hand, how you would tell which bootloader is present.
if your old UNO boards have the original 2k bootloader installed, while the newer ones have "optiboot" installed, this could account for the different behaviour you're seeing - and would place the blame for the failure squarely with the optiboot bootloader.
still, my original advice holds... use the internally configurable pull-up resistor on D7. or, if you must use an external pullup, connect the top end of it to a spare output pin (instead of Vcc) that you can set high once your own code has taken control.
regarding the developers ever reading these posts: i've never seen any sign of them here 