What causes menu to stop querying for children half way through menu I have a 'primary menu', rendered in one case using the 'bartik' theme (site preview)  and rendered in the other using the 'Bootstrap' theme. (site preview)

With the bootstrap theme, working from left to right the children are presented until 'Publications'. Then there are no children. The same menu presents all the children in Bartik all the way across. Looking through it, the children are not in the php data ($element[#below]) and are not printed out to the HTML. 

What is causing this?
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.