I don't think that preference has been used in a very long time. It used to display a one-time explanation of the icon that indicates a pop-up has been blocked.
You're probably looking for privacy.popups.showBrowserMessage instead, which controls whether or not an explanatory notification bar is shown whenever a pop-up is blocked (the indicator icon on the right side of the address bar is always shown when a pop-up is blocked).

• http://kb.mozillazine.org/About:config_entries

If you need to always allow pop-ups from a particular site, you can add it as an exception under Options - Content. See the following article for details.

• Pop-up blocker settings, exceptions and troubleshooting

Also note that Firefox usually displays an icon on the location bar if a pop-up is blocked.

Could you give more details about hat the problem with pop-ups is?