If I unplug all the USB connections to modify the computer (insert/remove pci card, etc) and replug the USB connections back into different locations, they do not work....at least not immediately. I have to reboot a few times, disconnect them, reboot, etc. and eventually they will be recognized and work fine.

However, if I disconnect everything, shut the power off and then reconnect them all in the same ports, all is fine. Is this normal behavior? I would have thought it wouldn't matter, but it does. Not sure if this is on the BIOS or OS side.