For some reason my top menu is completely empty but only on pages I just recently added from the master site using Articles Sharing (other Articles Sharing pages from the master site are showing the menu fine).

One thing I was doing was trying to hide the Home menu item because I am just going to make the Logo go to the home page, so I have two mod_mainmenus (second is disabled now but it still is having that problem). I tried to duplicate the extra mod_mainmenu setup on the slave site to match the master site. The second mod_mainmenu are both unpublished now on both slave and master.

Has anything like this ever happened to anyone else? Any ideas on how to diagnose it? Eventually I might be able to find the write code to trace in mod_mainmenu or multisites.

Thanks for any help you can provide.

I don't really know but perhaps you should check the module settings and see if the is present in the list of module and enabled.
Another idea could be to check the class used by the menu in the list module.