couple of things.
Pop up generators are often a different category than virus. They are closer to that category called spyware. Normally they arrive on your computer as a result of installing 'free' software - peer to peer file transfer is notorious for that as are some of the 'drivers' required to access some web sites. Some of the tool bars being distributed also carry some hidden payloads. Anti-virus software vendors won't include spyware/pop up in the virus category for fear of being sued. They have made a new category called 'malware' but you must opt in.
adaware is good. But beware of others, particularly those that pop up in an unsolicited fashion and warn you that your computer is unprotected. What better way to get at your computer than to offer to protect it for free.
If it is a true virus it will frequently disable the anti-virus software so that it can continue to hide even if you run a deep scan. If Defender does not find it boot in safe mode with network support and go to one of the online health check sites. My preference is ESET
http://www.eset.com/onlinescan/ imho defender is one of the ugliest of the malware products. If you want efficient and lightweight have a look at nod32. That being said, if you are running vista it is a realy pita to get rid of microsoft protection.