But compiz adds it back on top when a fullscreen window has no focus.
I'm guessing the problem is that Unity's panel window(s) are not created
in a way that allows compiz to keep them hidden (under full screen
windows) independently for each display.
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Yes, I can confirm that.
It also explains why some applications appear to be affected while
others are not.
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** Attachment added: output of xprop -root.txt
https://bugs.launchpad.net/unity/+bug/1457910/+attachment/4422552/+files/output%20of%20xprop%20-root.txt
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I'd like to add that my comment (#2) is not correct. The bug went away
for a while when I set the launcher to only show up on one display, but
the bug later began happening regardless of the option. It's
intermittent. Sometimes a program will go full screen correctly; other
times the Unity panels
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