Its a focus problem, not really Tk's fault. Your window manager determines which window has focus, by either "clicking on a window" or a sloppy mouse focus, where the window that the mouse is in, takes focus. Look in your window manger settings for focus type. Or Google for "your_window_manager focus"
It would be chaos on the desktop without focus.
You might want to redesign your app to be a single window, or at least tell us what you are trying to accomplish with this.
The problem is compounded by the menu doing a screengrab. You might want to read perldoc Tk::focus
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