I'm just guessing here, since I've never tried anything of the sort... but is one side set to read the clock from the cable and the other side set to send the clock? And are the clock settings matched on both sides (actually, SPDIF might not need this-- I think the clock info may actually be on the wire... I can't recall).
It's kinda weird... why would the card be sending any input directly to the output? Does the "click" go away if the coax isn't connected?