jamescooley1 is right. You should rip to the hard drive using the built in ripper within AnyDVD. Then try to work with the movie off the hard drive using DVDShrink.
This will normally work. If you still have a problem with one, try running the decrypted files on the hard drive through FixVTS. http://www.videohelp.com/tools/FixVTS Then try Shrink again.