X11 application's windows are managed independently of other windows.
By default when a new X11 window is opened it does not acquire the focus.
To acquire the focus
Edit ~/Library/Preferences/org.x.X11.plist.
search for these keys and
wm_focus_on_new_window : ACTIVATE THIS!!!
wm_ffm : focus follow mouse
wm_click_trought : the first click on an inactive X11 window activates it and the click event is passed to the application. When disabled the first click only activates the window, but is not passed to the application.
The focus after closing an X11 window IS STILL A MESS!
Source:
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