Here's a quick work-around. Many caveats included:
***
Change the indicator appmenu to to base the menu shown on window stacking
rather than solely on the input focus. This works slightly better under the
"sloppy focus" scheme.
There are, however, some caveats:
* I didn't test what happens with the usual click-to-focus
* There is no visual indication of which window has the menu.
* A patch to compiz is required to make the stacking be always up-to-
date.
* Always-on-top and desktop windows are still handled the old way.
The issue is that these windows never receive stacking changes,
and therefore the only way to deal with them is via the input focus.
Fixing this requires a complete separation of the menu focus from the input
focus --- this can only be done within Compiz, and the information should
from there be communicated to indicator-appmenu e.g. via a root window
attribute.
** Patch added: "Work-around -- use stacking instead of input focus for
tracking the menu"
https://bugs.launchpad.net/ubuntu/+source/unity/+bug/674138/+attachment/2084598/+files/indicator-appmenu-sloppy-v1.patch
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https://bugs.launchpad.net/bugs/674138
Title:
"Global" appmenu breaks sloppy focus
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