Audio Video not sync'd after transcode

[TKIII]

I looked for a problem similar to this Before posting but didn't find one, sorry if this is a repeat.
I have all the seasons of a show on dvd and have been ripping them to my computer for backup. for the first 5 seasons, the ripping was perfect, i was ripping to Mp4 with a video quality of 1024 and mp3 audio quality of 128 for a bit over 300 MB for each episode. When i got to the sixth however, using the exact same options as before, on three separate computers, the audio was 1200ms ahead of the video, i tried "synchronize on audio track" on the Preferences>Stream output>Sout stream>Transcode. i tried the seventh season and it did the same thing so i though maybe it was copy protection of some kind, i went to the tenth and everything worked fine on that season. is there a way of adding a permanent audio delay at transcode? or maybe rip the audio and video seperately and adding them back together using vlc? i have both linux and windows versions if there's any difference between them.

[Ghengis]

Probably not the place to be posting this, but have you tried Handbrake? If you're coming straight from DVD, I've found no better solution for MP4 transcodes. I use the PS3 setting, which works on my PC, XBox 360, *and* PS3 (the latter two streaming from TVersity). And I've never had the slightest issues with audio sync.