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My dock is on the left side of my screen & by default X11 Window Manager (wants to start at the uppermost left corner & it's always behind the dock. The X11 terminal app itself doesn't do this, but some of the programs I use have a default grey background (I believe like TWM), and these always start in the uppermost left corner behind the dock.

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Have you tried the current XQuartz version as replacement for bundled X11? – Daniel Beck Apr 5 '11 at 15:59
Yes, but it is a TWM problem, which comes bundled with XQuartz in case there are no other window managers to use. – churnd Apr 5 '11 at 17:54

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