ive had these exact same problems, but im not sure its to do with the files being avi.... i also dont think its to do with converting ntsc to pal... so far i managed to do oz seasons 1-6 and sex and the city seasons 1-3 with no problems, but ive had the exact same sync issues with lost season 1&2 smallville season 5 house md season 1 and my name is earl season 1 but only the episodes 13 and 14 which were seperate torrents to the season 1 torrent i found containing episodes 1-12. i hope someone finds a solution soon... im currently doing house md for a 2nd time trying loads of different methods, i'll post later if i get any good results....
if its with sound its because the avi file were interleaved wrong and the VBR MP3 audio stream is corrupt, the only way i have found to fix this is to remake the file from scratch by demuxing it into its audio and video elements and putting the corrected audio back with the video. Good luck. There is also a post with the same problem that you are having http://forums.afterdawn.com/thread_view.cfm/286600 .
