Williarob
Thanks for the update!
I just checked out the 50 GB star wars disk from here http://originaltrilogy.com/topic/Star-Wars-Despecialized-Editions-Custom-Bluray-Set/id/49995 and it has no issues with the subtitle sync. Again the fact that you have branching probably complicate things, but i wanted to point out that njvc swapped the subtitles in using multiAVCHD (and using the .SUP files from Threepio). Just in case that helps with your current conundrum.