Hey Marc,
Not sure if you’ve figured this out or not, but I thought I’d drop a line.
I haven’t deduced the problem down to its definitive cause, but I will say that the problem you’re encountering isn’t bc of Final Cut. It’s the method from which you are extracting clips from the DVD’s. I am working on a project that requires footage from two instructional DVD’s and new footage that was shot digitally. The project requires me to use footage from all three. I had to rip/extract the footage from the two DVD’s (using Handbrake). One method I did created the same problem you’re having: audio and video way out of sync although on the timeline they appear the same.
For some reason the video seems to lag a couple seconds strangely.
After I extracted (ripped) the footage a couple ways, I found one that worked without causing the problem. My flow requires me to make it an MP4 (as opposed to MKV). Take it into Compressor and gave it the ol’ 422.
What do you use to extract?