I have had this happen to me, but on two diffrent films.
When the sound is out of sync, it was because there was a small peice at the front (when there was no sound) that was corrupt, NVE skipped encoding these frames but did not take out that peice of audio so when it was done it was out of sync. My file was a DivX file so I used a program caled DivFix (found it onDoom9), that fixed the origional file and then everything was fine.
When I had the other problem, the disc would repeat about 5 frames every 2 mins, not bad but bloody annoying:a
When I looked at the origional file it was encoded in NTSCFilm format (NTSC resolution @29 fps) and NVE had problems converting this to PAL (25FPS). The solution was to tell NVE to encode as NTSCFilm. Go to the settings screen and change the format to NTSCFilm and see if that works:D