OK, I also found a way to get back the right focus behaviour, and I
think is proof that is related to *unity-window-decorator* <-->
*metacity* communication. Of course, only talking about Unity 3D.

1) Open a lot of windows and keep them at normal size on screen (NOT 
maximized); some if not all, will have the wrong focus behaviour as explained 
extensively above. ATTENTION: do not open programs that may corrupt data if 
closed directly, as we are going to reboot the system trough terminal later on.
2) Open a terminal window.
3) Run the command "metacity --replace"
4) Entire unity interface will disappear
5) All windows will be replaced by metacity compositor (which anyway is already 
running trough unity), including window borders. Shadows will be gone.
6) Magically, all focus behaviour will be correct now, and with the same theme 
in use. Of course cannot use ALT+TAB and unity launcher, top bar will be gone.
7) To restore the system from this situation, press CTRL+ALT+T to open another 
terminal
8) Do a "sudo reboot" command.

So, when unity-window-decorator is launching metacity compositor,
something is wrong in there, just my 0.02$.

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https://bugs.launchpad.net/bugs/885941

Title:
  Windows top bar focus transparency not behaving properly

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