Start XQuartz automatically on X11 app launch
I was having the same problem. Quitting XQuartz and deleting ~/.Xauthority resolved the issue for me.  I got the idea to do this from the Mountain Lion, Xquartz, and (lost) autostart thread in the Apple Mailing List. Other suggestions from that thread include:


Logging out and then back in after installing XQuartz.
Ensuring that the $DISPLAY variable is being set by by launchd and not clobbered by your shell scripts (see http://xquartz.macosforge.org/trac/wiki/X11-UsersFAQ#sshXforwardingdebugging)