Have you messed with the permissions for those pages? It's easy to hide resources from yourself. If that's the issue, the solution is to add yourself to all user groups.
Another possibility is that the resources have become invalid somehow. This happens sometimes when you drag resources around in the tree. Resources can had invalid parents, be their own parents, or two resources can be each other's parents. This will prevent them from showing up in the tree.
You may be able to find them with the search bar at the upper left of the Manager if you search by pagetitle. If not, you can find them in the DB.
SiteCheck will test all resources for validity, but I can't guarantee that that's your problem.
