It sounds like a mux (multiplexing) issue. 'Interleaving' is how the video and audio data are encoded into the file. Usually it goes in blocks:
1 sec of vid, 1 sec of audio, 1 sec of vid, etc. This makes it easy for a slow machine to 'keep up' without jumping around in the file, and if it falls behind, it's much easier to catch up.
But the spec allows it to be encoded any way you want. So if you're encoding video on the fly, some issues might make those blocks change sizes. For most modern computers playing back standard-def video this shouldn't be a problem. Winamp is just trying to optimize your experience.