The JavaFX launcher will call Toolkit.exit() when the application is done -- this happens when the last window is closed, or an explicit call to Platform.exit(), or if an exception is thrown from the init() or start() method. The QuantumToolkit shuts down the pulse timer and the renderer, then calls Application.terminate in glass.
This works fine on Windows.
On Mac, we frequently get an exception. This may be provoked by the toolkit continuing to use glass after the glass Application has been terminated.