Dug more here, and it's not metacity at fault at all.

Reproducion steps:       graphical bootup disabled,    It also happens in the 
first GDM login session.    If you click a name to start with, then the 
accessibility button is no longer interactive for clicks for some reason, and 
vice-versa, if you start by clicking the accessibility options,  mouse clicks 
are afterwards not directed to the name list.  Once you log in like this, the 
events only go to the top panel, no matter what WM I use.


Attaching strace to metactiy shows events on the socket (fd/11)  during mouse 
clicks, but no response happens.

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A while after login, mouse and keyboard events go only to a single window
https://bugs.launchpad.net/bugs/481053
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