You’re running into a combination of problems:
1. When you creat timelines in Encore 1.5 they are numbered in the order you create them (in 1.0, they are numbered backwards). The numbering is what the DVD player will use to seek the next chapter, and you can’t change the numbering once you’ve created the timeline.
2. The “next chapter” button is not strictly defined for the DVD spec when there’s no chapter points left in the timeline. Most DVD players will simply execute the end action, some will do nothing, some will jump to the next timeline.
The most effective solution people have found is to put an extra chapter point about a second before the end of each timeline. That way when the user presses “next chapter”, it will jump to that point and after a short pause the end action will execute.
Otherwise you’re stuck recreating all of your project’s timelines in the exact order you want.
Oh, also, I’ve seen a bug where if you have too many timelines in a project that are all linked from the same end action or override (for example, you have a transition from the menu that leads to all of them), Encore screws up the navigation. I think the limit is something like 42.