1) Here is the NPE exception:

Glass detected outstanding Java exception at +[GlassHelper ApplicationNotifyDidBecomeActiveMethod]:src/com/sun/mat/ui/GlassHelper.m:171
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
at com.sun.javafx.tk.quantum.PixelUtils.imageToPixels(PixelUtils.java:43)
at com.sun.javafx.tk.quantum.GlassSystemMenu.getPixels(GlassSystemMenu.java:267)
at com.sun.javafx.tk.quantum.GlassSystemMenu.addMenuItem(GlassSystemMenu.java:197)
at com.sun.javafx.tk.quantum.GlassSystemMenu.addMenu(GlassSystemMenu.java:118)
at com.sun.javafx.tk.quantum.GlassSystemMenu.setMenus(GlassSystemMenu.java:92)
at com.sun.javafx.scene.control.skin.MenuBarSkin.setSystemMenu(MenuBarSkin.java:107)
at com.sun.javafx.scene.control.skin.MenuBarSkin.access$8(MenuBarSkin.java:100)
at com.sun.javafx.scene.control.skin.MenuBarSkin$2.invalidated(MenuBarSkin.java:117)
at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:359)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:100)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:197)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.access$1(ReadOnlyBooleanWrapper.java:196)
at javafx.beans.property.ReadOnlyBooleanWrapper.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:163)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:130)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:163)
at javafx.stage.Window.setFocused(Window.java:345)
at com.sun.javafx.stage.WindowPeerListener.changedFocused(WindowPeerListener.java:65)
at com.sun.javafx.tk.quantum.GlassWindowEventHandler.handleWindowEvent(GlassWindowEventHandler.java:47)
at com.sun.glass.ui.Window.handleWindowEvent(Window.java:934)
at com.sun.glass.ui.Window.notifyFocus(Window.java:913)


2) Here is the code that causes it (Notice "A BAD URL" is used in one of the images):

package helloworld;

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */

import javafx.application.Application;
import javafx.beans.InvalidationListener;
import javafx.beans.Observable;
import javafx.beans.property.BooleanProperty;
import javafx.event.ActionEvent;
import javafx.event.Event;
import javafx.event.EventHandler;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.CheckMenuItem;
import javafx.scene.control.Menu;
import javafx.scene.control.MenuBar;
import javafx.scene.control.MenuItem;
import javafx.scene.control.RadioMenuItem;
import javafx.scene.control.SeparatorMenuItem;
import javafx.scene.control.ToggleGroup;
import javafx.scene.image.Image;
import javafx.scene.image.ImageView;
import javafx.scene.input.KeyCombination;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class HelloMenu extends Application {

    //private static final String imageURL = "file:src/helloworld/about_16.png";

    private CheckMenuItem showMessagesItem;

    @Override public void start(Stage stage) {
        stage.setTitle("Hello Menu");
        Scene scene = new Scene(new VBox(), 400, 350);
        final MenuBar menuBar = new MenuBar();
        //menuBar.setUseSystemMenuBar(true);

        EventHandler actionHandler = new EventHandler<ActionEvent>() {
            public void handle(ActionEvent t) {
                if (t.getTarget() instanceof MenuItem) {
                    System.out.println(((MenuItem)t.getTarget()).getText() + " - action called");
                }
            }
        };

        // --- Menu 1
        final Menu menu1 = makeMenu("_Debug");

// Menu menu11 = makeMenu("_New", new ImageView(new Image(getClass().getResourceAsStream("about_16.png"))));
        final Menu menu11 = makeMenu("_New", new ImageView(new Image("A BAD URL")));
        MenuItem menu12 = new MenuItem("_Open", new ImageView(new Image("src/helloworld/folder_16.png")));
        menu12.setOnAction(actionHandler);
        Menu menu13 = makeMenu("_Submenu");
        showMessagesItem = new CheckMenuItem("Enable onShowing/onHiding _messages");
        MenuItem menu15 = new MenuItem("E_xit");
        menu15.setOnAction(new EventHandler<ActionEvent>() {
            public void handle(ActionEvent t) {
                System.exit(0);
            }
        });
        menu1.getItems().addAll(menu11, menu12, menu13, showMessagesItem, new SeparatorMenuItem(), menu15);


        // --- Menu 11 submenu
        final MenuItem menu111 = new MenuItem("blah");
        menu111.setOnAction(actionHandler);
        final MenuItem menu112 = new MenuItem("foo");
        menu112.setOnAction(actionHandler);
        final CheckMenuItem menu113 = new CheckMenuItem("Show \"foo\" item");
        menu113.setSelected(true);
        menu113.selectedProperty().addListener(new InvalidationListener() {
            @Override public void invalidated(Observable valueModel) {
                menu112.setVisible(menu113.isSelected());
                System.err.println("MenuItem \"foo\" is now " + (menu112.isVisible() ? "" : "not") + " visible.");
            }
        });
        menu11.getItems().addAll(menu111, menu112, menu113);


        // --- Menu 13 submenu
        MenuItem menu131 = new MenuItem("Item _1");
        menu131.setOnAction(actionHandler);
        MenuItem menu132 = new MenuItem("Item _2");
        menu132.setOnAction(actionHandler);
        menu13.getItems().addAll(menu131, menu132);


        // --- Menu 2
        Menu menu2 = makeMenu("_Edit");
        MenuItem menu21 = new MenuItem("_Undo");
        menu21.setAccelerator(KeyCombination.keyCombination("ctrl+Z"));
        menu21.setOnAction(actionHandler);
        MenuItem menu22 = new MenuItem("_Redo");
        menu22.setAccelerator(KeyCombination.keyCombination("ctrl+Y"));
        menu22.setOnAction(actionHandler);
        // menu separator
        MenuItem menu23 = new MenuItem("_Disabled");
        menu23.setDisable(true);
        menu2.getItems().addAll(menu21, menu22, new SeparatorMenuItem(), menu23);


        // --- Menu 3
        Menu menu3 = makeMenu("_Radio/CheckBox");
        CheckMenuItem checkMI1 = new CheckMenuItem("_1 CheckMenuItem - checked");
        checkMI1.setSelected(true);
        CheckMenuItem checkMI2 = new CheckMenuItem("_2 CheckMenuItem - not checked");

        RadioMenuItem radioMI1 = new RadioMenuItem("_3 RadioMenuItem - selected");
        radioMI1.setSelected(true);
        RadioMenuItem radioMI2 = new RadioMenuItem("_4 RadioMenuItem - not selected");
        ToggleGroup group = new ToggleGroup();
        radioMI1.setToggleGroup(group);
        radioMI2.setToggleGroup(group);

        InvalidationListener selectedListener = new InvalidationListener() {
            @Override public void invalidated(Observable valueModel) {
                MenuItem mi = (MenuItem)((BooleanProperty)valueModel).getBean();
                boolean selected = ((BooleanProperty)valueModel).get();
                System.err.println(mi.getText() + " - " + selected);
            }
        };

        checkMI1.selectedProperty().addListener(selectedListener);
        checkMI2.selectedProperty().addListener(selectedListener);
        radioMI1.selectedProperty().addListener(selectedListener);
        radioMI2.selectedProperty().addListener(selectedListener);

        menu3.getItems().addAll(checkMI1, checkMI2, radioMI1, radioMI2);
// ImageView im = new ImageView();
// im.setImage(new Image(imageURL));
// cmitem.setGraphic(im);

        menuBar.getMenus().add(menu1);
        menuBar.getMenus().add(menu2);
        menuBar.getMenus().add(menu3);

// String os = System.getProperty("os.name");
// if (os != null && os.startsWith("Mac")) {
// Menu systemMenuBarMenu = makeMenu("MenuBar _Options");

// final CheckMenuItem useSystemMenuBarCB = new CheckMenuItem("Use _System Menu Bar");
// useSystemMenuBarCB.setSelected(true);
// menuBar.useSystemMenuBarProperty().bind(useSystemMenuBarCB.selectedProperty());
// systemMenuBarMenu.getItems().add(useSystemMenuBarCB);

// menuBar.getMenus().add(systemMenuBarMenu);
// }

        ((VBox)scene.getRoot()).getChildren().add(menuBar);
        stage.setScene(scene);
        stage.show();
    }

    private EventHandler showHideHandler = new EventHandler<Event>() {
        public void handle(Event t) {
            if (showMessagesItem.isSelected()) {
                System.out.println(((Menu)t.getSource()).getText() + " " + t.getEventType());
            }
        }
    };

    private Menu makeMenu(String text) {
        return makeMenu(text, null);
    }

    private Menu makeMenu(String text, Node graphic) {
        Menu menu = new Menu(text, graphic);
        menu.setOnShowing(showHideHandler);
        menu.setOnShown(showHideHandler);
        menu.setOnHiding(showHideHandler);
        menu.setOnHidden(showHideHandler);
        return menu;
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
// com.sun.javafx.Logging.getFocusLogger().setLevel(PlatformLogger.FINE);
        Application.launch(args);
    }
}