Use an attached application and steps to reproduce :

1. Launch the application. There is menuBar.
2. Select : menu 1 -> Menu 1 SubMenu 0 -> Menu 1 SubMenu 0 SubMenu 0 -> Menu 1 SubMenu 0 SubMenu 0 MenuItem 0
3. Click ToggleButton "Use system menu bar". MenuBar will be moved to SystemMenuBar
4. Select the same location from 2 : menu 1 -> Menu 1 SubMenu 0 -> Menu 1 SubMenu 0 SubMenu 0 -> Menu 1 SubMenu 0 SubMenu 0 MenuItem 0

I see double last menu : one - system one, and one - FX one. And exception on net beans.

Exceptions thrown :

Glass detected outstanding Java exception at -[GlassRunnable run]:src/GlassApplication.m:97
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
at com.sun.javafx.tk.quantum.PopupStage.getOwnerScene(PopupStage.java:58)
at com.sun.javafx.tk.quantum.PopupScene.sceneChanged(PopupScene.java:46)
at com.sun.javafx.tk.quantum.GlassScene.setGlassStage(GlassScene.java:266)
at com.sun.javafx.tk.quantum.ViewScene.setGlassStage(ViewScene.java:78)
at com.sun.javafx.tk.quantum.PopupScene.setGlassStage(PopupScene.java:36)
at com.sun.javafx.tk.quantum.PopupStage.createTKScene(PopupStage.java:64)
at javafx.scene.Scene.impl_initPeer(Scene.java:716)
at javafx.stage.Window$10.invalidated(Window.java:742)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:107)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:141)
at javafx.stage.Window.setShowing(Window.java:809)
at javafx.stage.Window.show(Window.java:824)
at javafx.stage.PopupWindow.showImpl(PopupWindow.java:402)
at javafx.stage.PopupWindow.show(PopupWindow.java:347)
at javafx.scene.control.ContextMenu.doShow(ContextMenu.java:280)
at javafx.scene.control.ContextMenu.show(ContextMenu.java:254)
at com.sun.javafx.scene.control.skin.ContextMenuContent.showSubmenu(ContextMenuContent.java:862)
at com.sun.javafx.scene.control.skin.ContextMenuContent.access$2000(ContextMenuContent.java:90)
at com.sun.javafx.scene.control.skin.ContextMenuContent$8.changed(ContextMenuContent.java:815)
at com.sun.javafx.scene.control.skin.ContextMenuContent$8.changed(ContextMenuContent.java:807)
at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:347)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:177)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.access$100(ReadOnlyBooleanWrapper.java:147)
at javafx.beans.property.ReadOnlyBooleanWrapper.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:143)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:108)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:141)
at javafx.scene.control.Menu.setShowing(Menu.java:179)
at javafx.scene.control.Menu.show(Menu.java:375)
at com.sun.javafx.scene.control.GlobalMenuAdapter$3.invalidated(GlobalMenuAdapter.java:85)
at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:135)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:177)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.access$100(ReadOnlyBooleanWrapper.java:147)
at javafx.beans.property.ReadOnlyBooleanWrapper.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:143)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:108)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:141)
at javafx.scene.control.Menu.setShowing(Menu.java:179)
at javafx.scene.control.Menu.show(Menu.java:375)
at com.sun.javafx.tk.quantum.GlassMenuEventHandler.handleMenuOpening(GlassMenuEventHandler.java:41)
at com.sun.glass.ui.Menu.notifyMenuOpening(Menu.java:187)
Glass detected outstanding Java exception at -[GlassRunnable run]:src/GlassApplication.m:97
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
at com.sun.javafx.tk.quantum.PopupStage.setVisible(PopupStage.java:97)
at javafx.stage.Window$10.invalidated(Window.java:772)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:107)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:141)
at javafx.stage.Window.setShowing(Window.java:809)
at javafx.stage.Window.hide(Window.java:834)
at javafx.stage.PopupWindow.hide(PopupWindow.java:416)
at javafx.scene.control.ContextMenu.hide(ContextMenu.java:294)
at com.sun.javafx.scene.control.skin.ContextMenuContent.hideSubmenu(ContextMenuContent.java:868)
at com.sun.javafx.scene.control.skin.ContextMenuContent.access$1900(ContextMenuContent.java:90)
at com.sun.javafx.scene.control.skin.ContextMenuContent$8.changed(ContextMenuContent.java:812)
at com.sun.javafx.scene.control.skin.ContextMenuContent$8.changed(ContextMenuContent.java:807)
at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:347)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:177)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.access$100(ReadOnlyBooleanWrapper.java:147)
at javafx.beans.property.ReadOnlyBooleanWrapper.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:143)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:108)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:141)
at javafx.scene.control.Menu.setShowing(Menu.java:179)
at javafx.scene.control.Menu.hide(Menu.java:392)
at com.sun.javafx.scene.control.GlobalMenuAdapter$3.invalidated(GlobalMenuAdapter.java:87)
at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:135)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:177)
at javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.access$100(ReadOnlyBooleanWrapper.java:147)
at javafx.beans.property.ReadOnlyBooleanWrapper.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:143)
at javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:108)
at javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:141)
at javafx.scene.control.Menu.setShowing(Menu.java:179)
at javafx.scene.control.Menu.hide(Menu.java:392)
at com.sun.javafx.tk.quantum.GlassMenuEventHandler.handleMenuClosed(GlassMenuEventHandler.java:46)
at com.sun.glass.ui.Menu.notifyMenuClosed(Menu.java:193)