WordPress has just instated a global update to how menus work. It is no longer trivial to have pages that are hidden from the menu (and custom menus appear to be entirely disabled). As a result I will be working on the site architecture so that the default menu will at least approximate something I would be comfortable with.
If menus appear or dissapear, or if pages jump around between menus, this is why.
(Also, the main Header Image appears to be stuck on the default image. If this persists I may need to change to a different design)
EDIT: 7/27 – Customized Header Images and Menus are now saving properly. However, I may still use this opportunity to revisit the site architecture.