If i open the popup by clicking the button of the attached demo programm, i get the following error:
The program 'java' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadDrawable (invalid Pixmap or Window parameter)'.
  (Details: serial 552 error_code 9 request_code 55 minor_code 0)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)

public class Main extends Application {

    @Override
    public void start(final Stage primaryStage) throws Exception{
        final BorderPane borderPane = new BorderPane();
        final Button button = new Button();
        button.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent actionEvent) {
                Popup popup = new Popup();
                popup.getContent().add(new TextField(""));
                popup.show(primaryStage);
            }
        });
        borderPane.setCenter(button);
        primaryStage.setScene(new Scene(borderPane, 300, 275));
        primaryStage.show();
    }


    public static void main(String[] args) {
        launch(args);
    }
}