I've recently been testing mods. In some cases I've found them to be not suitable and deleted them off Mod Organiser. Now, it's just come to my attention that at least some are still showing up in the right hand plug-in window, even though I've deleted them in the "Installed Mods" window! Anyone know what's wrong, why the plug-ins are still showing in the right hand window? Is my MO corrupted?

You'd be better off posting a comment in the nexus thread for MO. I don't think you'll get much in the way of help here...