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After using a fresh OS X system for a while, I regularly hit the point where X11 clients start and run, but their windows do not show up anywhere.

I suspect it has something to do with Mac port paths, but i am not sure. Has anyone else experienced this?

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I have recently installed ghostscript and for some reason X11 starts whenever I use gs, but no windows appear. Not sure if my issue is related to yours, but I'm interested in a solution as well :-) – neoneye Oct 18 '10 at 17:37
This sounds similar, indeed. – LennyAskDifferent Oct 19 '10 at 13:38

It might be a bit of a workaround, but you could try installing XQuartz, a newer version of X11. It bypasses X11 rather than replacing it, so you should be able to uninstall it again if you want Apple's X11 back.

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