The free version of DVD Rebuilder splits the movie into segments and encodes as a whole sequence of separate AVI files, based (I think?) on DVD chapters. It then joins all the video segments together when it creates the VOBs.
The problem here is that when a new segment starts the frame counter gets reset to zero - so the frame number for the subtitle filter is never reached. And of course if you use the "correct" frame numbers the subs will come up in every segment, not what you want!
Might need to use DVD Rebuilder in 3-click rather than 1-click mode and edit the AviSynth script for that segment individually. Unless someone can think of a better way of doing it?