Pop-up Blocker Not Working in Safari

As the title says, I have Block Pop-ups checked in system preferences, but I still regularly have pop-up windows. These windows don't appear on top of my Safari Window, but when I go into Mission Control or the App Expose (not sure if its still called that?), I can see them.
Normally its that piece of junkware mackeeper. I dont appreciate seeing crap like that, but I can't find a way to natively block it!
I haven't used GlimmerBlocker yet as I very much would prefer a native solution. I tried to find a setting in safari where I can individually block pages by domain name but I wasnt able to find that either. Can anyone provide a native solution for this? Or any other solution. Thanks!

I have been to websites that when you click somewhere on the content, doesn't matter where, it will open a popup ad. No real way to block that since you are "allowing" the window by the click. It only happens on the first visit of the day. It is more commonly tied to the dismiss X button on an overlay that requests you to join the site or sign up for something the site offers.
The click could possibly be blocked by a javascript blocker, but I imagine they are put up by the site and not redirecting from another server. So, you'd have to block the entire site's javascript.

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Hello,
'''Try Firefox Safe Mode''' to see if the problem goes away. Safe Mode is a troubleshooting mode, which disables most add-ons.
''(If you're not using it, switch to the Default theme.)''
* On Windows you can open Firefox 4.0+ in Safe Mode by holding the '''Shift''' key when you open the Firefox desktop or Start menu shortcut.
* On Mac you can open Firefox 4.0+ in Safe Mode by holding the '''option''' key while starting Firefox.
* On Linux you can open Firefox 4.0+ in Safe Mode by quitting Firefox and then going to your Terminal and running: firefox -safe-mode (you may need to specify the Firefox installation path e.g. /usr/lib/firefox)
* Or open the Help menu and click on the '''Restart with Add-ons Disabled...''' menu item while Firefox is running.
[[Image:FirefoxSafeMode|width=520]]
''Once you get the pop-up, just select "'Start in Safe Mode"''
[[Image:Safe Mode Fx 15 - Win]]
'''''If the issue is not present in Firefox Safe Mode''''', your problem is probably caused by an extension, and you need to figure out which one. Please follow the [[Troubleshooting extensions and themes]] article for that.
''To exit the Firefox Safe Mode, just close Firefox and wait a few seconds before opening Firefox for normal use again.''
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