Comment 12 for bug 848115

Out of desperation I did a format/reinstall. This problem does not exist out of the box. While reconfiguring the system to my tastes, I kept my eye on if/when it would reappear.

One aspect of my configuration is that I have a sandbox user that I run the browser out of, along with other potentially dangerous network applications, which is part of my active desktop session as my main user. I use(d) the avant-window-navigator as a launcher for the sandbox user.

Once avant-window-navigator was running, the focus problem returned in full force. I "fixed" this by starting the sandbox session into gnome-terminal instead, and launching things from the command line (which I tended to use more anyway). I don't know if the problem was AWN, or just some very unhappy interaction between two panels running at the same time. In any case, AWN is not running and the problem has not returned.

Hopefully this is helpful to others who ran into this very frustrating problem.