Dang, I'm sorry to see that it's not working properly - definitely was when I tested loading subpages from the previous version. Can you try sending me a copy of that project that you're working with so I can take a look at it? I might be able to fix both the bug as well as your project so you don't have to start over.
Copying and pasting between instances of MasterPlan is an interesting idea - I can see about putting that in the todo list.