This is because you're only a member of 3 sites. As a super admin you have the ability to view the full site list via the network admin, but that doesn't mean you're a part of every site.
The admin bar menu only lists the sites you're a member of, not the full list, that's how it's intended to work. Otherwise users would see sites listed that they have no ...
I solved this by following the instructions here;
I turned out that the .htaccess file was loading an old version of php as follows;
# Use PHP55
AddHandler application/x-httpd-php55 .php