Are you using Windows 7?
I had this problem too, overloads of mods installed and I couldn't get rid of them. The shit started when I switched over to Windows 7, just install your game to another direction and it should be fine.
Since I installed it to another direction it has been working great, alot of minor issues has disappeared too. So if you have your game installed in "Program (x86)" or any other place, just move it to another direction.
Kind Regards,
Jimmy Cuneo.