Usually, when your soundcard is built onto your motherboard, when you install a "second" one, it just overrides the one on the motherboard. I don't know if that helps out any, but that's what I've noticed.
I also had a similar problem where when I tried to record sound not from a mic but what sounds I "hear" (using Camtasia). I played the video back and it hadn't recorded any audio at all, even though nothing was muted on the windows' volume control. So then I discovered a second sound panel that had installed with the soundcard that was overriding all of my settings on the default volume control.
Hope that helps you out a bit.