Hi Pete,
It is probably due to dummy titles used as a counter piracy measure and is explained here:
http://trac.handbrake.fr/wiki/SupportFAQ#scrambledscenes
Anyways.
To identify the correct title to encode in Handbrake do the following:
1 – Insert disc into PC
2 – Open Handbrake
3 – Click SOURCE to scan the disc
If the disc comes back with 99 Chapters
Open VLC
Play disc as if I was going to watch the movie
When movie begins, click PLAYBACK, drop down and click TITLE to see which title is playing
Close VLC
On Handbrake main screen, Select the title that was playing on VLC
Issue Resolved
If the disc has the standard amount of chapters; rip as usual
4 – Done
– source
The bottom line is you need to find the original title that is playing and load that in Handbrake to avoid the dummy files.