FULL PRODUCT VERSION :
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 6.1.7601]

A DESCRIPTION OF THE PROBLEM :
MenuBar/MenuBarSkin causing memory leak if tried to be removed from a scene. See code part from jdk8u121 code of com.sun.javafx.scene.control.skin.MenuBarSkin (from line 371):
Utils.executeOnceWhenPropertyIsNonNull(control.sceneProperty(), (Scene scene) -> {
            scene.getAccelerators().put(acceleratorKeyCombo, firstMenuRunnable);

            // put focus on the first menu when the alt key is pressed
            scene.addEventHandler(KeyEvent.KEY_PRESSED, e -> {
                if (e.isAltDown() && !e.isConsumed()) {
                    firstMenuRunnable.run();
                }
            });
        });

This is the most probable cause that the event handler is not weak so it is never removed so if menubar applied on a scene graph (e.g. via FXML).

This issue is raised and solved in openjdk: https://bugs.openjdk.java.net/browse/JDK-8166950

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Create a stage with a scene and within that a control that has internal MenuBar; after disposing the control it will remove in memory, as menubar will be refer to the topmost scene.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Control and MenuBar should be garbage collected.
ACTUAL -
Control and MenuBar stays in memory after GC

REPRODUCIBILITY :
This bug can be reproduced always.

CUSTOMER SUBMITTED WORKAROUND :
No, we do not use MenuBar for sections of disposable content.