I did that one with DVDDecrypter, version before last. IIRC, I had it set for aggressive structure protection removal, remove PUOs, hmm, and I think detect mastering errors. Probably the latest version of DVDDecrypter will be okay with defaults.
BUT... DVDShrink threw a memory error on the ripped files. So I reauthored and used Start/End Frame option, jumped to chapter two and went backwards to 2 seconds. That became the start point. Thereafter everything went as normal and the backup (main movie only, of course) plays through fine.
There's most certainly a bunch more ways to do it. Try again and good luck.