I tried removing the pull-ups on three of the failed units. One unit was once again able to communicate on UART2, the other two were not. I am not sure what to conclude from this, other than to mention that the two that were unrecoverable are older. Could continued operation with this double pull up arrangement lead to a permanent failure of the pins?
The OS we are using is generally Windows XP, although occasionally Windows 7 pc's are also used. I don't think the terminal log would be of much use, as I don't receive corrupted serial data when these failures occur, there is just no received data at all.