If you're running one of the comcast motorola boxes, I think I know what's going on. There's a bug in those boxes where it gets stuck on 2 channel when you watch 2 channel programming, and won't switch over automatically for 5.1 content. Try cycling the power once the opening credits start rolling, that fixes it for me.

This kind of crap happens with the Moto DVR HD boxes a lot when recording, and it's a big pain in the @ss. Motorola has yet to fix it, AFAIK. Hope the suggestion works for you, let us know.