Click start, then run, then type in services.msc and then hit Ok. On the list to the right you'll find a bunch of stuff that's running, scroll down until you find Messenger and right click it, and go to Properties. Click Stop, then where it says Startup Type choose Disabled, then apply and ok.
It's not spyware you're getting, that's why all the anti-spyware programs aren't helping. Windows has a built-in messenger thing that was supposed to be for legitimate network messages and stuff but I'd say there's a 99.9& chance you won't miss anything with that disabled except for those pop-ups.
If that doesn't work then post again and we'll sort it out
