I have a similar problem too where my Audigy Value card lowers my wave bar all the way to 0 when I'm pausing a movie and the fact that it can't mix things like my winamp and wmp as lets say for example, I play a movie on wmp and then I pause on it and start winamp. No music is playing and when I check my wave bar in the sound card settings, its been pushed to zero and until I unpause the movie and resume it, the wave bar moves all the way back up. I did the same thing and scanned for spyware/adware/malware/virus' and nothing! So I don't know what to tell you
I'm living with it rite now as this only happened when I reinstalled my OS because of a hardware change I had to make.