I have a similar problem, but for some reason, if I create an ad-hoc template, all the other pages using the same template also get the same ad-hoc template. Our structure is like this:
Project Index (menu item page type with repeater)
- project 1 (custom page type)
- project 2
- project n
The problem is that the project index and each project page (the client has already created 100s of them) are using the same template. We need to get the Project Index page to have a separate template.
Do I just create a new Project Index page from scratch with its own template, and then move all the project pages over into that one?
Update so I've just discovered that all of the pages that we're having trouble with are set to "Inherit from parent" under the Template tab. Is there any way to change this setting in bulk, instead of having to change it on 100s of individual pages?