Why do X11 applications start but their windows stay invisible? 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?
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.