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The value for
privacy.popups.disable_from_plugins doesn't have to be 2. It can be any of the following four:
0 = Allow all popups from plugins.
1 = Allow popups from plugins, but limit the number of popups to
2 = Block popups from plugins.
3 = Block all popups from plugins, even on whitelisted sites.
If you decide to allow popups, either regular ones or plugin popups, I'll suggest setting the value of
dom.popup_maximum to a reasonably low number, such as 2. The default value in Firefox is 20, but there aren't many legitimate reasons for a web page to launch more than two popups at a time, and definitely not 20!
dom.popup_maximum already exists, so just find it in the pref list, right click it, select
modify, and set the new value to 1, 2, or something reasonably low. This will prevent the unfortunate occasions where your screen will be filled with majorly unwanted and often gross popups that refuse to go away.