I would also check to see if there is an extra .js file or text file sitting outside of the root folders aka admin, cont, includes. I have 3 sites I have to do the same thing to. Good luck to you robimx.
They are not even close to 100% operational. They are more than likely the ones cause the banners popping up while they try to close this door that got opened. I have some .htaccess errors myself with other plug ins on a few sites that are not making sense. I would say wait a bit to deactivate it or reinstall just in case there is something left. But you can always deactivate all the other plug ins and see if that fixes the banners. I have had to turn off shopping carts due to false sales being generated.
Are you on a godaddy hosting account?
