Maybe someone is guessing that they affect
SEO negatively. It would be based on the idea that having too many outgoing links is not good. Google gives this warning while logged into their Google Webmaster service. Also pop-ups are not good. It's like this: I know pop-ups are not liked, and too many outgoings shows that you are not keen to keeeping customers around, likely 'cause you are not an intelligent person. I am guessing.
Also I would not put the sign-up form on the index page, 'cause signing up is secondary. First you have to give someone a reason to sign-up, like show your compentance or something.