Try running the file with different MPEG-4 codecs. It may be that there's nothing actually wrong with the file.
For example, I have a couple of film clips that somone did up using XviD, which is that zany (buggy?) open-sourced alternative to DivX 5. If you play the files using the DivX codec, even with no post-processing, really weird artifacts start showing up.
Play it using the XviD codec and suddenly the artifacts are gone. So maybe you don't actually have a cruddy file 😀
With all the alternatives out there and deviations from what's supposed to be a standard, I don't think that any of the MPEG-4 implementations (be it Windows Media, Quicktime, DivX, or other) are going to actually last and become mainstream. DVD is only now really mainstream, and since you have to spend a lot of effort making that transportable it plays in favour of movie companies. Maybe by the time they come out with MPEG 5 or 6 and everyone is running a 64-bit or 128-bit processor platform and it doesn't take 9 hours to encode a movie it'll catch on.
I mean now it takes under a minute to encode an MP3 straight off a CD, at 320 kbps VBR with a new(er) computer. I remember when such a feat required 20-25 minutes at least, not counting manually ripping the WAV off the CD first, and all you could get was 160 kbps CBR encoding.