I have similar issues with both Firefox 25.0.1 and Thunderbird 24.1.1. I
have multiple extensions installed on both, but neither has a single
same extension (so either this may be caused by multiple different
extensions or something else is going on).

Additional info:

- I have been hit with this problem every now and then since around
Firefox 10 and Thunderbird 3. I think this is a problem in Ubuntu XUL
core because the problem is visible with both Firefox and Thunderbird.

- I have been hit with this problem using at least Gnome 2.x, Unity and
Cinnamon desktop environments so I'd guess this is not related to the
window manager. I haven't used KDE long enough to verify if this problem
is visible in that environment, too.

- Since I have reduced the system latency(*) I've hit this problem more
often; I guess it's some kind of race condition between some paraller
threads or processes doing something. The system is running on i7-3770k
with HT enabled (without overclocking).

(*)
mira@desktop:/proc/sys/kernel# grep . sched_*
...
sched_latency_ns:200000
sched_migration_cost_ns:500000
sched_min_granularity_ns:100000
sched_nr_migrate:3
sched_wakeup_granularity_ns:50000

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https://bugs.launchpad.net/bugs/1231588

Title:
  Firefox windows don't accept focus

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