We'll create fresh WordPress site with WP Custom Menu Filter Plugin installed. You have 20 minutes to test the plugin after that site we'll be deleted.
WP Custom Menu Filter Plugin uses a new filter hook in WordPress 3.1 that allows Custom Menus to be filtered. Instead of using the generic CSS {display:none;}, this plugin actually excludes nav menu items from even being created. While it uses the CSS class tag in the Custom Menu to determine which custom menu items should be excluded, it does not use CSS to hide the menu items, which savvy users can discover. Instead using one custom menu, the user can hide portions of their custom menu to visitors (even the savvy ones) while revealing other portions of their menu to users who are logged in and vice versa.