How can this be?

Could be a nasty ground loop - not affecting optical links, a software
problem causing crappy resampling on your PC or a
poor/mismatched/defective/... digital output on your ITX board.

Which Via ITX board are you using ?

It's the EPIA 800.
http://www.viavpsd.com/product/epia_...therboardId=21

How can I determine if grounding is the problem? None of the other
equipment (3 amplifiers, 1 DAC) seems to exhibit any poor grounding
symptoms, but I seem to recall that when I hooked up the analog outputs of
the computer to the amplifier inputs directly it gave me "alternator whine"
(even though other analog sources didn't). Should I try an isolating
transformer on the coax to see if that fixes it? Any other ideas?