When a java window that has focus is closed occasionally focus will be completely lost.
This is on a RH9 box, with metacity v 2.6.2.
To reproduce run SwingSet2, go to the OptionPane demo, click on one of the buttons to bring up an OptionPane, and close it, repeat this, often times when closing the optionpane focus will not go back to SwingSet2 as is expected. This is particularly annoying when you using keyboard accelerators to close a window.