Yes, I did watch back a burned DVD and the problem is still there.
Yes, I did sync it up in Final Cut Pro, then exported it out through compressor (and even tried as a plain old .AIFF file) and when I drag it into DVD studio Pro, unaligned with the same video I synced it to. Again it’s in various places, not just the whole thing being off, it will be on in one place, and off in another. But if I go back to my FCP timeline… both of those places are on and are fine.
This is just really bizarre!