The attached test case demonstrates that JFXPanel prevents a Swing application from terminating normally when all windows are disposed. System.exit must be called or a TERM signal must be sent using Control-C (if run at a command prompt) or by "kill -term <pid>". I have produced this in both Linux and Windows.

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import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javafx.application.Platform;
import javafx.embed.swing.JFXPanel;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.SwingUtilities;


public class ShutdownBug {


    public ShutdownBug() {
        final JFrame frame = new JFrame("JavaFX 2 in Swing");
        final JFXPanel jfxPanel = new JFXPanel();
        frame.add(jfxPanel, BorderLayout.CENTER);
        final JButton button = new JButton("Exit");
        frame.add(button, BorderLayout.NORTH);
        button.addActionListener(new ActionListener() {


            @Override
            public void actionPerformed(ActionEvent e) {
                Platform.exit();
                frame.dispose();
                /* Process does not terminate without this or sending a TERM
                 * signal or pressing control-C. */
// System.exit(0);
            }


        });

        final Runnable runnable = new Runnable() {


            @Override
            public void run() {
                System.out.println("Running shutdown hook.");
            }


        };
        final Thread shutdownThread = new Thread(runnable, "shutdown-hook");
        Runtime.getRuntime().addShutdownHook(shutdownThread);
        /* Neither makes a difference. */
// Platform.setImplicitExit(true);
        Platform.setImplicitExit(false);

        /* Closing the window has the same problem. */
        frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        frame.setSize(500, 500);
        frame.setLocationRelativeTo(null);
        frame.setVisible(true);
    }


    public static void main(String[] args) {
        SwingUtilities.invokeLater(new Runnable() {


            @Override
            public void run() {
                new ShutdownBug();
            }


        });
    }


}