It happens once a a GREAT while. I don't really understand why either. When it does, I use the start/end sliders and make 2 DVD's out of the original movie. I've seen this mostly on stuff with lots of menus etc. (and they get wiped out - using my method). In my case, I've always gotten a warning durning the initial quick scan, and the DVD's had far too many audio tracks.
Yes, in your case that (ac3 -2 ch) is the audio for the movie and you need it.