You need to get things the way you want them in the View Map view, save it as a view or "Get current window's settings" to update the view if it already exists. It is best to have saved Layer Combinations, Model View Options etc in these views (not "Custom" in any category) so things don't get mixed up. Then place the view on your layout, and all should be good. (Don't place the project map viewpoint on the layout)
If you have to unlock (turn on?) layers each time in the view map this is the problem.
