I’ve had something similar happen, that’s why I asked about DVDSP. In Studio Pro, I ended up removing all the chapter markers on the Track, reimported my new asset, and placed it on the track. It fixed the problem, I was able to view the whole thing. My best guess is that it had something to do with GOPs. So maybe the encode didn’t stop 30 seconds early…maybe it was DVDSP not seeing the whole thing because of a chapter marker (or some other marker–compression/score). Have you tested the mpeg somewhere else? Mpeg Steamclip – or even in a Finder preview window?
Jim