You seem to have corrupted your applications.menu somehow. `rm ~/.config/menus/applications.menu` should fix that. The replacement of Preferences and Administration with GNOME Control Center has nothing to do with alacarte.
Please tell me if this fixes your problem. ** Changed in: alacarte (Ubuntu) Assignee: (unassigned) => Travis Watkins Status: Unconfirmed => Needs Info -- Alacarte crashes and missed menus https://launchpad.net/bugs/79205 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs