I just updated to version 1.3.1 and suddenly there are menu items for custom post types I created that I can't move or delete. When I do so and save from Admin Menu Editor, they come right back. Specifically they are custom post types I had moved to be submenu options for one main menu item. It's as if the custom post type has to have an element on the main level of items.
Make sense? Any idea what would cause this--it's been working fine up until now.