This is an odd problem, and unfortunately I'm not familiar enough with using a PC as a transport for multichannel sources to have any particularly good advise.

It sounds like the 990 is seeing something odd about the input signal if it is excluding surround modes from the list. Have you tried using the surround mode buttons on the remote to change modes while the source is playing? I'd be curious to know if the 990 allows Pro Logic IIx that way. Also, have you made any changes to the source computer?

I'd definitely also try playing a DVD to see what the 990 does with that.