Java and JavaScript are 2 different things. Anyway its probably being blocked and sounds like you've turned notification off (it does get a bit annoying doesn't it?).
To allow pop-ups in IE7 on the menu bar go to Tools > Pop-up blocker. Then either turn it off (temporarily), or if you visit the site alot go to the Pop-up blocker settings option and add the site you wish to allow to the allowed sites list (incidentally you can also re-enable the notification here too)