This is the fourth Multi-site I have set up and we ran into this a couple of times before -- two errors:
* My sites pop down does not show full list of sites (only primary site) in admin. or front end
* Front end pop-down has same problem, but does not show second level menus (Dashboard; Sites, etc.)
The * - Wildcard is set up, as are all .htaccess and wp.config settings.
Recommendations and trouble shoot appreciated.