I'm not sure if other people had the same problem, but I just had a killer time fixing this problem, so for all people also lost out there.
What happened: When upgrading manually from 271 - 284a suddenly my admin account ( superuser ) was denied access to all sites beside the main blog and the blog admin stuff disseapered.
How come? : After a while I figured out the site_admins option in wpmu_sitemeta was like this:
a:1:{i:0;s:5:\"admin\";}
Apparently this didn't bother the old code or somehow it got set when upgrading, I'm not sure.
Solution: update site_admins field with this: a:1:{i:0;s:5:"admin";} without the " and it's fine again.