I was able to duplicate it after building and running the "Mail Status Control.app" [1].
The short java program below seems to be sufficient. If you don't set apple.awt.UIElement to true it steals focus from all programs (as you'd expect); if you do then it only steals from X. If I have it running in the background once a second, it only steals focus the first time it runs after I click in an X window. I have focus-follows-mouse set and just moving the cursor between X windows doesn't make it steal focus. Regarding Jeremy's comment "there must be *something* I could do put XQuartz in a mode that would prevent this focus loss", it can't be that all other applications explicitly do something for this. Either they start up in some way that makes it happen automatically, or there's something XQuartz does to *allow* its focus to be stolen. The fact that it only happens after clicking in a window suggests that it's the latter: when a window is selected in that way something must happen that allows a single focus-stealing to happen, and it doesn't happen when it's selected by focus-follows-mouse. I hope this helps someone track it down. Here's the program: import javax.swing.*; public class Javabg { public Javabg() { JPanel panel = new JPanel(); } public static void main(String[] args) { System.setProperty("apple.awt.UIElement", "true"); new Javabg(); } } -- Richard -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.