Having our app (creator), when invoking the popup, the focus gets transferred to JRootPane.
That doesn't seem to be correct and has probably more flaws in the focus handling impl:

1) Why it is transfered to the JRootPane in this case,
2) How come that JRootPane, which is not 'visible to user' component can get the focus at all.

You can debug it in the creator this way:
When you start from console, and enabling the output to the console (launcher switch -J-Dnetbeans.debug.console=true), then during working with the IDE when anytime you press Ctrl-Shift-Pause(orBreak), you get dumped the currect focus owner into the console.
Invoke (almost) any popup menu, and press the shortcut, and you'll see in the console the focus owner is JRootPane.