As I’ve fallen foul of this twice in as many days (I must be having one of those weeks) I thought it worth mentioning in case anyone else does the same thing!
When creating a custom post type, the code works as expected but suddenly the Pages disappear from their respective menu. They are still counted:
…but otherwise don’t exist in the Dashboard. The problem here is using the custom post type “order”, although no mention is made of this in the Codex as a reserved post type.
The solution is to namespace your post types (e.g. jem_order), which has the added advantage of avoiding conflicts with other plugins too.