Fixing Unity's New Windows Not Coming to the Front on Ubuntu
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If you use Firefox in fullscreen as much as I do, you’ve probably hit the same problem I have.
What happens is this: while I’m browsing fullscreen in Firefox, I click some other popup window and it opens underneath Firefox instead of coming to the front. WiFi status, uploading images to Weibo, all sorts of stuff.
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And it only happens under Unity. Annoying as hell.
Well, there’s a fix now.
Install and launch compizconfig-settings-manager:
sudo apt-get install compizconfig-settings-manager
General Options - Focus & Raise Behaviour - Focus Protection Level
Set it to “Off”

That’s it, done.
Source: Fix For Some Apps Starting Behind Focused Windows In Ubuntu (Compiz)
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