Comment 1 for bug 1244397

Kuni H Iwasa wrote:
> Gimp, which also uses x11, does not have this problem.

Note that current official GIMP packages do no longer use X11 - they are all built with the Quartz backend of GTK2. Do you have any other GTK+ applications installed which use the X11-backend of GTK+?

Possibly related: a XQuartz issue with multi-monitor setup on Mavericks just discussed on the X11-user mailing list
<quote>
On 2013-10-24 10:40 +0200, Jeremy Huddleston Sequoia wrote:
>> Um... I installed Mavericks on a two-monitor system today, and
>> after finding (in what's becoming an Apple tradition) the
>> unlikely location of the controls for freeing the displays to act
>> as they have since OS 6 or so (that is, one large, contiguous
>> piece of pixel real estate), was able to run an animation that
>> spans the two displays, as the system has since 10.6.
>>
>> The controls I used were in the System Preference pane for
>> Mission Control. I unchecked all boxes, but the relevant one is
>> "Displays have separate spaces." Doing so also allows application
>> windows to span displays, instead of fading out on one.
>>
>> (…)
>
> Yes, disabling that checkbox returns you to a "legacy mode" of sorts.
> XQuartz will behave nicer with multiple monitors in that mode, but
> you will loose out on all the useful updates to multi-monitor
> support.
>
> This incompatibility with multi-monitor support is a known issue, and
> the fix requires changes to both XQuartz (specifically libXplugin)
> and OS frameworks. Unfortunately, this means that I won't be able
> to address the bug with an XQuartz update, and you'll have to wait
> for the OS-side of the solution in a future OS update.
>
> Hopefully the "disable Displays have separate spaces" workaround will
> be a satisfactory stop-gap until the issue is fixed in a future
> update.
</quote>
<http://lists.apple.com/archives/x11-users/2013/Oct/msg00003.html>
(the reply doesn't seem to be available in the ML archives yet)