You may have two sound boards on the system...one motherboard integrated and the other a sound controller slotted to the motherboard bus. Windows is supposed to be smart enough to sort this out and disable one or the other, however there are occassons when this is not the case.
I too have athe exact problem with a flight similator station I built that has 5.1 w/ subwoofer. I have had it six months and have only been able to get the integrated sound working correctly OR just the two front speakers of the 5.1...no bass, no sub-woofer, no mid. When I got the mid, bass and sub going the front two speakers would stop working. I just gave up and have resided myself to just getting teh sound through the integrated sound by way of the motherboard.
I cannot offer any help that makes sense or solves the problem you are having but I can certainly share your pain.