I never had sync issues at all. I have encoded via handbrake and autogk
Steps:
1. Use DVD Decrypter in IFO mode, enable stream processing and choose Direct Stream Copy for each disk. This will give you a muxed Mpeg2/AC3 file for each disk
2. Join the two files with MPEG Video Wizard from Womble or Video Redo.
3. Now you have one big muxed MPEG/AC3 file. Encode it with what ever you want...simple and ALWAYS works. You do not need to trim anything.
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