OP, if you are talking about using the receiver to expand to seven channels, the PCM-ness of the incoming signal should not be a problem as the receiver would decode any dolby or similar signal to PCM before performing any EQ, channel expansion etc. If your computer is sending the stereo sound as if it were multichannel (with silence in the center, surrounds and LFE) the receiver will not extract the extra channels because it thinks they're already there. They actually are there, technically. You can have the same problem with some OTA broadcasts which will send a stereo soundtrack as DD5.1 so that the receiver can't or won't expand it. It should be easy enough to see if the Yamaha thinks it's getting multichannel input when you send a stereo program . . . but IDK exactly where the relevant display is.
To the extent you don't get a good answer here, since it could be a computer issue, I'd suggest asking on the HTPC forum.