navigation permissions roles

Three times now, several items in our primary navigation and other menus have disappeared for site admins, authenticated and anonymous users. (User 1 still seems to be able to see/access these areas of the site.) Even when you navigate directly to the URL, all users aside from User 1 get an Access Denied message. This has happened at least 4 times, and we're not sure of the reason or exactly how its resolved. The first time it happened was after we migrated data from an external database into our site (including users and other nodes). We're unsure of the cause the second time.