Thank you Omer for the feedback. My system is fully updated, even with
all proposed updates. I am not a newbie of Linux/Ubuntu, I have plenty
of programming experience as well. If you need any help in
debugging/verifying I can help, this issue is really small but much
annoying because it disturbs an otherwise very good experience.

The updates did solve one of the issues, the one related to the "Scale"
plugin in compiz that cut out the title bars if the windows was outside
view. But focus issue remain there, as per message #19 above.

I have installed Emerald on Unity from sources, have also modified a bit
to better understand how events are handled, and issue of focus is not
there in Emerald, so it should not be related to how events are sent by
the underlying window manager system, it merely is a unity-window-
decorator/metacity issue.

Another note that may be helpful, on gnome-shell problem is not there,
focus is always behaving properly. I seriously doubt is due to the theme
as well, as it happens with any theme.

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

Title:
  Windows top bar focus transparency not behaving properly

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