I've stopped using Pop-up Stopper and switched to "Ad Popup Killer" which basically stops Messenger Popups and all other popups. Simple in design but very effective.
Ad Popup Free 3.50 - Free version
http://download.com.com/3000-2378-10...ml?tag=lst-3-3
Ad Popup Killer4.0 - Paid version
http://www.safefirewall.com/popupdownload.html