What soundcard and speakers have you got? I presume in every combination of your setup only the subwoofer is working? If that's the case it sounds like it's either your speakers or your amplifier (generally located in your subwoofer) and the signal isn't being redirected through properly. I'd suggest trying a pair of headphones on each jack at the back of your soundcard (except the subwoofer channel) just to rule that out, and then try using the headphone jack on the 5.1 system too just to be sure, but I'd say it's not routing the sound through.