My system is super clean I can assure you.
I'll try to explain the problem a little more.
When I type msconfig, everything works fine. Never said there was something wrong with msconfig.
In the window that opens from msconfig, there is a tab that tells you wich programs or applications will start when Windows starts.
There, I can click an item to either activate an application or deactivate it so it won't start when Windows opens.
After, when I click ok, I get an error message that I don't have the administrator rights to do so. Never had this problem before. In safe mode, I will still get the message but at least, everything works.