That would concern me. Before you do much else, at least verify continuity for every pin on your newly-socketed machine to the next component in line. You may well have damaged a pad or trace during your removal-and-socket procedure on that box. If youve damaged a FREDDIE connection, that will affect the validity of the test results.
Yep - double checked the continuity of the 40 pin socket and everything is good. No shorts either between pads.
Will have another closer look at it next weekend.