Like you, I love Firefox for many reasons, including its popup blocking support. It turns out that some clever people figured out that you could launch popups from Flash, getting around the Firefox default settings.

Fortunately, you can get around it:

1. Type about:config into the Firefox location bar.
2. Right-click on the page and select New and then Integer.
3. Name it privacy.popups.disable_from_plugins
4. Set the value to 2.

The possible values are:

0: Allow all popups from plugins.
1: Allow popups, but limit them to dom.popup_maximum.
2: Block popups from plugins.
3: Block popups from plugins, even on whitelisted sites.

Note: Borrowed from http://www.petebevin.com. Read the original article.