I'm no php artist but I've been handling WP for over three years pretty well, recently I came here to ask a bit of help because of a server change that didn't really worked out. So I'm kinda not a noob user but not really a programmer. Hope this helps a bit to deal with the explanation over here. :)
The thing is, recently, after upgrading to 3.4.1 I noticed that the SuperAdmin Panel is not there. I tried to go in the [site]/wp-admin/network with the accounts that are SuperAdmins but all of them seem to don't have access anymore. Every SuperAdmin account receive the "you don't have permission to access this page" message.
I dug in some old threads to look for an answer and did deactivate my plugins to update WP for 3.4.1, also, tried to deactivate all the plugins to see if it was going to solve it and nothing change and also checked out for the tables that should be there and all of then are.
Also, I check the database for the userlevels and both SuperAdmins are userlevel 10.
I didn't find any solution after some hours of research so I'm here to ask for the 'Sword of omens give me sight beyond sight', ;)