its probably a codec thing. As much as people like to think VLC will play everything it may not have the codec you need for that particular file correctly. some codec packs Ihave only seen on PC like the CCCP codec pack. here are a few things that might help you figure it out and/or fix it.
MplayerOSX 1.0pre 8 (another good player)
Divxdoctor II
DivxTool
also try downloading the latest xvid codec and divx codec and try to play in quicktime
None of this may work as I have never heard ofthe issue you have but they may.