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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.
1Have you tried the current XQuartz version as replacement for bundled X11? – Daniel Beck – 2011-04-05T15:59:55.540
Yes, but it is a TWM problem, which comes bundled with XQuartz in case there are no other window managers to use. – churnd – 2011-04-05T17:54:08.087