Finally got it to work with DVD-Rebuilder Pro.
The problem is that the free version of DVD-Rebuilder inserts the trim() function before any custom functions (such as subtitles), resetting the frame count to zero. The Pro version inserts it after the custom functions meaning that things like subtitles can use absolute frame numbers.
Now, has anyone done the same thing for Empire and Jedi? Really want to get some decent anamorphic versions of these with decent looking subs on them. If anyone has... can they post the subtitle scripts? :-)