DVD editing problem/ bad tracking in wmp and vlc

Ok, to start I've been trying to edit together some video clips in Womble Video Wizard DVD. The source video is mostly DIVX 5@29.97 w/ mp3 audio , XVID @25 w/ mp3 audio and some MPEG2 at 29.97 footage w/ mp2 audio. Everything is working pretty well, but when I encode the whole bit for some reason it doesn't track properly in wmp or vlc. I encode it as mpeg2 program at rez 720x480, 29.97 fps, with ac3 audio at 320kbps, high quality, 9/16 pixel aspect ratio, everything else default.

In WMP it almost has no idea how to track, and if I try to skip ahead in the video say 1 minute, its playing video from the 20 second mark. In vlc it handles it a bit better, except for some reason certain video clips play faster, especially the mpeg2's (which are all the same source). However ALL of the video plays faster than the parts with only audio.

I tried Quickstream Fix from VideoRedo, no help.

I demultiplexed it in TMPG Enc and then tried to remultiplex it. It spit out some error like "X s packets cause buffer overflow - The MPEG file might cause error when played". But still processed the video. Alas, it still didn't track properly.

When playing the split m2v in VLC, the fast tracking is still present. When playing the audio in VLC, its sounds as it should and tracks well.

Any help?