Well, it's not THAT much of a stretch, if (a) MC didn't completely uninstall itself, or (b) during the install, MC changed some defaults in the way the underlying media player played back. Neither seems all that improbable; I can count on one hand the number of programs I've ever seen that don't leave SOME trace of themselves, whether in the registry, "shared" DLLs that they were the only user of, etc. In fact, I just checked, and JRiver does leave at least a small piece of itself behind: HKLM\SOFTWARE\JRiver\Media Jukebox\Plugins\Help File. Obviously that's not affecting playback, but it's not unreasonable to wonder whether there are other uninstall bugs.
I did double-check that WMP doesn't have automatic levelling enabled, at least visibly, but I do wonder if there's something like that that's causing this. It seems to happen more on playback of material with pauses in it, which supports that theory. Whether that's happening in WMP, or the driver, or wherever, and whether MC caused it or was just coincidentally installed around the time it started happening, it's hard to say.
It certainly could be a hardware problem, but I'd be hard-pressed to imagine what could go wrong with a cheapie 2.1 PC speaker set (Cambridge Soundworks) that would result in random, stereo, smooth one-second fade-ups and fade-downs. If the hardware volume knob were at fault, I'd expect crackling and jitteriness when I turn it, and I don't get that. I've also tried pounding on the outside of the knob and it's not affecting the volume at all. If an amp component were failing, I'd expect it to affect one speaker or the other, not both, and again I'd expect to hear crackling or bandpass limiting or clipping or SOMEthing other than a smooth, slow stereo fade.
This is a weird one.
Jay