Just in case G-Force doesn't follow this thread I've posted the question in his GOUT Stabilisation thread so hopefully we should get a reply soon. :)

I am inclined to agree with what Darth Malwalker said about using PgcDemux when PGC_2 comes first like on the GOUT DVDs. The reasons I say this is that I had problems syncing the audio and had to offset it by about 12 frames which I didn't understand at the time but do now ;) Also when I used VobBlanker I only replaced PGC_1 and left PGC_2 as it was, this means that PGC_1 on my DVD would be at least 12 frames longer then on the GOUT DVD so by using PgcDemux I should be replacing like for like. There is also this guide by oldschooljedi which directs you to use PgcDemux rather than the VOBs direct.

Until I am certain that I have ironed out all these little issues I am putting Empire and Jedi on hold, it is also likely that there will be a V2 of Star Wars.

@Jonno
Many thanks for the further info / explanation I am 99.9% sure I can do what you say using Final Cut Pro, Compressor & DVD Studio Pro if I get stuck I will give you a shout if you don't mind ;)