It's actually ignoring what I tell it.

I disabled it because I use a third party popup blocker and Firefox's is nothing but trouble because I have to whitelist sites on-demand, which might work normally but now sites are rendering their windows with popups that are not ads - i.e. login boxes and such, and it's a pain to keep having to allow. So I disabled it. Well it's still blocking popups. It's not the third party blocker, because it's not set to block any popups from sites that I authorized fully. Just to verify I disabled the third party and clearly saw Firefox blocking the popup even though I removed the "Enable Popup Blocker" checkbox.