membership access levels and pages

I just ran into an issue that I need assistance with. I have a custom menu set up for my primary menu, so I can have a nice menu structure with sub pages, etc. I just tried to hide certain pages when a person is logged out and certain pages when a person is logged in, but it seems as though the page only gets hidden if you are not using a custom menu. I turned my menu off, and the pages hide from the nav bar, but when I am using my custom menu, the pages do not get removed from the nav bar.

Is there any way to fix this? I need to use the menu I created as the promary navigation, but I need control over showing and hiding those pages.