Hi Francis,
This only seems to happen with native system buttons (like the Aero glass ones), and not when we fully chrome the window and use WPF buttons as the title bar buttons. I'm not sure this is something we can control though because when a WPF Popup is open and you click those native title bar buttons, the system doesn't seem to register the click for some reason. However if you click on any WPF buttons or controls, those clicks are registered.