Kmon, same problem here with Disaster Movie - another bad DVD - I used DVDFab to rip DVD to hard drive (i.e. DVD to DVD). No problem. VOB files are intact, movie plays when VLC is pointed at the directory - the movie is definitely there. But when fab analyzes it through the DVD to mobile option, the main movie doesn't show up.
Your hunch that it might be something with the IFO files is worth investigating. I'll try copying just the VOB files to another directory, and using IFO Edit to rebuild the IFO files, and see if I can point Fab at directory with the original VOB's, and the rebuilt IFO's, and see if it picks up the main move. I will report back on that.