This is a long question. I use the 990 connected directly to my HTPC. The HTPC does it all--plays DVDs, plays digital and analog TV, plays games, plays music. So all output is via the onboard ALC882D Realtek HD audio chipset on my motherboard, connected with a Toslink to OPT1 on my 990. If I am watching TV, on my 990 screen, the following are lit up(shown in the order they are on the Display:
Dolby Auto
PCM ProLogicII
Digital

With a DVD, I see only Dolby Digital ProLogic

I switch the music to upsample or bypass and it works fine.

What got me wondering about audio was trying to output 5.1 from the game Battlefield 2. They have a hardware option which I checked, and I was missing the center(which I don't have--990 set to "none") audio, and the rears. I then went to the Realtek software to see what I could change. On digital, it simply offers sampling rates(44, 48, 96, 196(?)) and whether SPDIF out is enabled or not. If I use their own test where the bee flies around the room, it is only present left and right front, no rears, and no center zone, despite setting it for 5.1. So why is the chipset not outputting a straight digital signal to the 990? Should it not just send data to the 990, which will do any necessary decoding?
What about the PCM I see on the display--what does that indicate about the output of my HTPC?

I guess I am confused about exactly what is coming out of my HTPC, and whether I should be getting something different/more/??? I do not see any place where I can get a SPDIF passthrough, which I think would be best.

Any help appreciated!