My powered sub actually already has the internal crossover bypassed, and while I don't regularly listen to any analog sources I have used them on occasion without any full-range to the sub. On the other hand, I've got the 990 set up as a 7.1 system. I'm getting the same issue you are with subwoofer settings when either center or surrounds are off, but I didn't have a chance to try leaving it in that state and playing an analog source. I've got a green building meeting tonight after work, but I'll try to do a comparison between my current arrangement (7.1) and your setup with an analog source in stereo mode.