What kind of AVI files are they? WiMP and MC both use the DirectShow engine, and should both output essentially identical quality. Knowing what kind of AVI files (what codec was used to compress the video stream inside of them) might help.
A geuss without knowing that... One thing that might be happening is that MC might be using a different Video Renderer than WiMP. Vista does have a new Video Rendering Mode, which WiMP will use if your video card supports it. Check here: Options --> Playback --> DirectShow Playback Settings, select AVI under DirectShow Filters (right hand side), and hit Select Filters. Wait a second because MC seems to freeze when loading the DirectShow Playback Settings dialog. Then try changing the Video Renderer from the dropdown menu. MC defaults to VMR9 which should really be the best possible option, but maybe your video card or drivers are stinky at VMR9 mixing for some reason. Try switching this to VMR7 first, and if that doesn't work, try Legacy (usually called Overlay mode).
EDT: I actually found some references in a quick google search to quality problems with nVidia's Vista drivers and VMR9 playback modes (surprise, surprise -- add one more way that nVidia's Vista drivers stink), so if you have an nVidia card this might be it.