As discussed on the mailing list in thread "JFXPanel ignores size change of root node" the following is a workaround to force a JFXPanel to resize itself when the scene's size has changed:

          Scene scene = getScene();
          setScene(null);
          setScene(scene);
          invalidate();

In the attached testcase this seems to work for about 70-90% of all attempts. Adding a sleep between setScene(scene) and invalidate makes it 100%. On my core i5 with 2.6 Ghz the 10ms sleep is enough while 9ms is not. YMMV.