Ok so I went to change access to a couple of our menus - to the recruiting which I was trying to make officer only, and to the shout box which I was trying to take off of public access. I edited the menus and changed the access level on the drop down menus - but the menus are still viewable by everyone.
This is because you have advanced layout options enabled. When you use Advanced Layout Options, the Menu placement and visibility is controlled in the layout file.