To 'Re-author' the movie using DVDShrink is to copy only the main movie without the 'extras', that will also take away the 'menu' in the movie. There are no 'hidden' subtitles or anything, that's just silly. If your using DVDShrink, which I'm using to copy this movie as I'm typing, all the subtitles in the movie, appear in the analysis.
This is usually easily solved by just enabling the subtitles during the movie with your remote. I've had this sort of glitch before with subtitles not appearing on their own as they do on the master disc.