The problem you are describing, is one I have seen when trying to rip DVDs with an extra layer of protection against ripping. The way I understand the problem is the the DVD directory is intentionally written with errors. These errors cause Handbrake-GTK (and several other ripping programs) to find 99 tracks on the disk. One of these will be the correct one, and the others will be dummies. These errors don't seem to affect a DVD player because it gets instructions from the menu how to find the right data.
Disney DVDs are especially likely to have this extra protection.
I have read that Handbrake reads the track information from the menus and shouldn't have this problem. My experience is that it still has problems. I have also read in the Handbrake support forums that there are more clever and faster solutions to avoid this problem, but I have not been smart enough to make them work.
When I run into this problem I resort to capturing the stream out of VLC (a media player). It takes longer and is certainly processor intensive, but VLC can capture a high-quality stream with numerous options for encoding. VLC plays the disk like a regular DVD player and doesn't seem to have the same issues.
-Shlep'