It is starting to make sense now. NTDETECT test the int 11h flag, and then it tries int 15h function C2.
Maybe if the PS/2 mouse flag is clear, it assumes there is no mouse port. Moving the mouse causes unexpected data to arrive at the port and causes a hang (mouse and keyboard both use port $60, yes?)
If the flag is set but int 15h fails, then it assumes no mouse is connected?
Maybe a different sort of patch in NTDETECT would straighten it out. What is the date and size of your NTDETECT.COM?
Must be a crappy mobo then.
I'm under the impression that it is a board which didn't originally have any PS/2 port, but was modifed to add one.