What causes menu to stop querying for children half way through menu
this is what i see. There are no children missing. Have you cleared your Browser cache?

Some themes need the parent item set to "expanded". The setting is available (e.g. http://example.com/admin/structure/menu/manage/main-menu)for every menu item but only parents need it. 


  Show as expanded. If selected and this menu link has children, the menu
  will always appear expanded.


This is the only wild guess i can take from your informations.