Did you capture the AC3 soundtrack direct from the LDs, or use the two-channel audio output through the ADVC110?
I'm not sure if the Boba Feta version captures the AC3 or not.
I have an ADVC100 and was going to trial this AC3 capture with mine (I have a new audio card with SPDIF input), as part of the SE releases were the re-mixed soundtracks.
Also, did you do any adjustments to the video using VD/AVISynth? (I have not seen it yet - am getting it from Myspleen at the moment).