I recently started having a problem on my iMac with xquartz 2.7.7 on os x 10.9.5 involving X11 window focus.
Whenever I click on an X11 window, active or inactive, after a few seconds that window loses focus, then the mouse pointer briefly becomes the spinning color wheel, and focus returns. It's an annoying delay approaching 10 seconds, for what used to be nearly instantaneous
I've tried using a different mouse, a different keyboard, re-installing xquartz, and disabling a dashboard client with error messages in the logs, but nothing has helped.
Several other Macs I use do not have this problem with xquartz, with either os x 10.8.x or 10.9.x
I haven't had much luck with web searches on this topic so far, just a couple false trails for similar but not identical problems.
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