If you have two xterms, and one of them is focused, then clicking on the other one behind something does bring it to the foreground.
So another workaround is to click one xterm first, and then click the one you want to focus. The first xterm will stay in the background, but it will cause X11 to gain focus, and then the second click will bring the second xterm to the foreground.
Its almost like X11 needs to have focus, before it will show the windows.
Clicking on the X11 Icon in the dock also brings all xterms to the foreground.
Do you think that I have a configuration issue, or have I found a bug? I am running in rootless mode.
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I have noticed this same behavior as well. I noticed it when I had 2 rdesktop sessions open with some other native windows. I now do a Shift-Command-Tab to get back to my X11 window when moving to another native window.
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