Just fixed some problems with MT 3.0. I was not able to control 1 weblog anymore. No user had really access to it anymore and there was 1 weblog where no user was attached anymore. The weblog was not displayed anymore but still noticed in the config of Movabletype.
With the help of the wonderful tool: MT-MEDIC I solved the problems.
Cleaning up the database with inactive non used weblogs and adding permissions to the users for 1 specific weblog.