As was stated elsewhere in this thread, I would suspect the Windows USB drivers for that motherboard.

Whenever you re-install Windows, you have to spend some time getting all of the correct hardware drivers. One of the most common things you'll need is drivers for your motherboard chipsets, such as USB and IDE. If these aren't properly updated after a Windows re-install, you'll often have strange troubles like you described.

Ruling out hardware/disk trouble with the Mk1 is also a step you should take.