Filip,
It sounds like -clean didn’t do its job, please see this thread: http://www.myeclipseide.com/PNphpBB2+file-viewtopic-t-3252-highlight-perspectivename.html
Keep in mind that after deleting the <eclipse dir>/configuration directory you will likely need to re-add MyEclipse as an extension via the Help > Soft Updates > Manage Configs mechanism and then restart. You should be back in action after that.