I did another install of 4.6.1 and the notifications seams to have caused another issue on the new server. Applications that depend on notification being there -- forums, blog, ect -- they all give errors concerning notifications.
This was eventually resolved by restarting the server two times. I think that the issue may be with the order that the applications are installed. I really scewed things up on my last server by trying to uninstall (unmount and delete) notifications. I trashed my database but I learned a lot...