Last night i got fed up enough that I went looking for a solution, other than blocking Flash in general since I do find it useful on many sites, and I found this page.
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.
It has worked fairly well for me so far, sites I know I got pop-ups on, I'm not.