Unfortunately you fail to mention which codecs/filters BS.Player actually uses for playback: this is shown by BS.Player (with a video file loaded!) under (Rightclick >) "Options" > "Filters" > (Advanced).
It appears that DivX6.x has some features which can play strange tricks on its users. You could try if rolling back to DivX5.2.1 solves the problem.
Alternatively try using BS.Player's internal AVI splitter. (Hold down SHIFT while clicking on 'Filter management' in preferences and check 'Use internal AVI splitter').