My msi board wouldn't let you have 5.1 speakers if the front panel audio was enabled (using a jumper on the motherboard). If the fpa was on, it would disable one of the inputs at the back. That's worth checking out.
i hate realtek. if the sound quality wasnt dia, i would happily go back to AC97, the issue is that these are standard issue on most new system, so almost everyone has both the windows sound control and the realteks. (But im an audio nut and spent £180 sound interface.
however i think the guy above was right, about front pannel audio. if all else fail pick up the cheapest X fi card you can get that deal with 5.1 and the sound quality will also be better.