It almost sounds like you are receiving messenger spam popups. This is a service that can easily be turned off. Go into your administrative tools, go to services, go to messenger and open it. Set service to disable on startup and stop the service.
If you don't feel comfortable doing that then get this program, as it will do it for you: Stop Messenger Spam
I would suggest that you run spybot S&D and AdAware malware removers while in safe mode also. It works a lot better that way.

Edit: Here is a site that will explain messenger spam to you.
Messenger Spam Site