I’m afraid this won’t help,
I’m afraid this won’t help, other than the “misery loves company” factor, but I posted a similar complaint about a WMA 5.1 audio track in a WMV file here: http://thegreenbutton.com/forums/p/95990/512026.aspx#512026
Works perfectly in WMP, but not in WMC. Absolute slience from the Microsoft crowd when I know there’s someone there who can explain the issue. Not sure why we’re getting the silent treatment on this one.
Reading in more detail, it does seem your situation is slightly different since you went from 5.1 Dolby to 7.1 PCM. I suppose you already confirmed that the “Allow applications to take exclusive control of this device” and “Give exclusive mode applications priority” is set on your playback devices -> properties -> Advanced tab? If not, it may be forced into shared mode, which cause it to go through the software mixer.