Hi musicmatt - welcome to the forum.
Firstly I have backed up National Treasure (PAL R2) with no problem. What I think has gone wrong is you have selected the wrong audio track when shrinking the movie. Personally I have not used DVDShrink, but I am sure someone who has will tell you how to select the correct track. It could be you have selected the DTS track and if you don't have a DTS compliant player, it will default to any other audio track on the disc. Other thought is that you have included all the tracks and all you have to do is press the audio button on you dvd player.
I could suggest you try other programs, but you seem to be going okay with what you have got, once you get over this wee problem.