A while back, XFree86/XDarwin fixed a problem whereby the rootless mode had the zeroeth y-position at the zeroeth screen position, instead of being just below the menu bar. It seems Apple's X11 implementation has this same bug, the only work-around for which is to make sure all geometries have +22 for the y-position and that you don't accidentally move a window too high up so that its title bar is obscured by the menu bar.
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