Im encoding my movie to via quicktime and end up with out of sync movie towards the end.

I rip the movie to elemenatry streams and mux them into 4 gb dvd stream chunks via mmt. Import the black pict into Qt then drag the muxed files over. Export to mpeg 2.

This process has been working great but lately movies are ending up out of sync at the end of the movie. Has this happened to anybody else that follows this process. Does anybody have a solution?