Tom, is it possible that you have a SDK and firmware mismatch? Please check the release notes from the GHI SDK install location (c:\program files(x86)\etc etc) and see what version of firmware is expected. Even then, I would suggest you go through the firmware update process to ensure you have everything matching, because that seems unlike any other issue we’ve seen.
(you don’t happen to have a second Fez device attached do you? that’s about the only other thing I can think of!)