I have a circular popup menu with a number of buttons which launches based on the location of the mouse on the screen. I am using Java 17 and JavaFx 22.0.1. The popup works well however my issue is the the pane is annoyingly still visible and noticable when you mouse down to the taskbar in windows. Here is the core elements of the code

 @Override
    public void initialize(URL location, ResourceBundle resources) {
        popup = new Popup();
        initializeCircularMenu();
    }

    
}


private void hideMenu() {
        if (popup != null) {
            popup.hide();
        }

        // Hide using CSS visibility
        circularMenuPane.setVisible(false);
        circularMenuPane.setManaged(false);

        // Ensure the pane is removed from its parent
        StackPane stackPane = ui.getStackPane();
        if (stackPane.getChildren().contains(circularMenuPane)) {
            System.out.println("Removing circularMenuPane from parent: " + stackPane.getId());
            System.out.println("Parent before removal: " + stackPane.getChildren());
            stackPane.getChildren().remove(circularMenuPane);
            stackPane.layout();  // Force layout pass
            System.out.println("Parent after removal: " + stackPane.getChildren());
            System.out.println("Is circularMenuPane in scene graph: " + stackPane.getChildren().contains(circularMenuPane));
        }
    }

    public void showMenu(Double x, Double y, PrimaryController ui) {
        this.ui = ui;
        this.clickX = x;
        this.clickY = y;

        // Calculate the map coordinates
        Point2D point = new Point2D(x, y);
        Point mapPoint = ui.getMapView().screenToLocation(point);
        Point wgs84Point = (Point) GeometryEngine.project(mapPoint, SpatialReferences.getWgs84());
        coordinates = wgs84Point.getX() + "," + wgs84Point.getY();
        int uniqueId = createUniqueCode();

        // Set the size of the circularMenuPane
        circularMenuPane.setPrefSize(RADIUS * 2, RADIUS * 2);

        // Add the circularMenuPane to the stackPane if not already added
        StackPane stackPane = ui.getStackPane();
        if (!stackPane.getChildren().contains(circularMenuPane)) {
            System.out.println("Adding circularMenuPane to the stackPane: " + stackPane.getId());
            stackPane.getChildren().add(circularMenuPane);
        }

        circularMenuPane.setManaged(true);
        circularMenuPane.setVisible(true);

        // Set the popup content and show it
        popup.getContent().clear();
        popup.getContent().add(circularMenuPane);
        popup.setAutoHide(false);
        popup.show(ui.getPrimaryStage());

        // Adjust the popup to be centered on the click coordinates
        double paneCenterX = circularMenuPane.getPrefWidth() / 2;
        double paneCenterY = circularMenuPane.getPrefHeight() / 2;

        double offsetX = clickX - paneCenterX;
        double offsetY = clickY - paneCenterY;

        double additionalOffsetX = 45; // Based on the offset seen in previous results
        double additionalOffsetY = -100; // Based on the offset seen in previous results

        popup.setX(offsetX - additionalOffsetX);
        popup.setY(offsetY - additionalOffsetY);

        System.out.println("Click coordinates: (" + clickX + ", " + clickY + ")");
        System.out.println("Popup set to: (" + popup.getX() + ", " + popup.getY() + ")");
        System.out.println("Pane center: (" + paneCenterX + ", " + paneCenterY + ")");

        popup.getContent().get(0).setOnKeyPressed(event -> {
            if (event.getCode() == KeyCode.ESCAPE) {
                hideMenu();
            }
        });
        popup.getContent().get(0).requestFocus();
    }

    private void initializeCircularMenu() {
        circularMenuPane = new Pane();
        circularMenuPane.setId("circularMenuPane");
        circularMenuPane.setPrefSize(RADIUS * 2, RADIUS * 2);

        // Add a black circle at the center
        Circle centerCircle = new Circle(RADIUS, RADIUS, 10, Color.BLACK);
        circularMenuPane.getChildren().add(centerCircle);

        // Add menu items with labels below the icon
        for (int i = 0; i < NUM_ITEMS; i++) {
            double angle = 2 * Math.PI / NUM_ITEMS * i;
            double xButton = RADIUS + RADIUS * Math.cos(angle) - 50;
            double yButton = RADIUS + RADIUS * Math.sin(angle) - 50;

            Button button = new Button(buttonLabels[i]);
            button.setShape(new Circle(10));
            button.setMinSize(100, 100);
            button.setMaxSize(100, 100);
            button.setStyle("-fx-content-display: top; -fx-font-size: 10px;");
            button.setWrapText(true);
            button.setTextAlignment(javafx.scene.text.TextAlignment.CENTER);

            String iconPath = getIconPath(i);
            if (iconPath != null) {
                ImageView icon = new ImageView(new Image(iconPath));
                icon.setFitWidth(35);
                icon.setFitHeight(35);
                button.setGraphic(icon);
            } else {
                System.err.println("Icon not found for button: " + buttonLabels[i]);
            }

            button.setLayoutX(xButton);
            button.setLayoutY(yButton);

            final int index = i;
            button.setOnAction(event -> handleButtonClick(index));

            circularMenuPane.getChildren().add(button);
        }
    }

I have tried the following: 
CSS: 
.center-circle {
    -fx-fill: black;
}

.button {
    -fx-background-color: lightblue;
    -fx-border-color: blue;
    -fx-border-radius: 15px;
}

.pane {
    -fx-background-color: transparent;
}

#circularMenuPane {
    visibility: hidden;
    opacity: 0;
}

#circularMenuPane.visible {
    visibility: visible;
    opacity: 1;
 private void hideMenu() {
        // Check and remove the circularMenuPane from its parent
        Node parent = circularMenuPane.getParent();
        if (parent != null) {
            System.out.println("Removing circularMenuPane from parent: " + ((Pane) parent).getId());
            ((Pane) parent).getChildren().remove(circularMenuPane);
            circularMenuPane.setVisible(false);
            circularMenuPane.setManaged(false);
            circularMenuPane.getChildren().clear();
            System.out.println("Menu hidden and pane removed from parent");
            // Force a refresh of the parent container
            ((Pane) parent).layout();
        } else {
            System.out.println("circularMenuPane has no parent");
        }
        popup.hide();
    }

private void hideMenu() {
    if (popup != null) {
        popup.hide();
    }
    
    // Debugging output to trace parent and children
    Pane parent = (Pane) circularMenuPane.getParent();
    if (parent != null) {
        System.out.println("Removing circularMenuPane from parent: " + parent.getId());
        System.out.println("Parent before removal: " + parent.getChildren());
        parent.getChildren().remove(circularMenuPane);
        System.out.println("Parent after removal: " + parent.getChildren());
    } else {
        System.out.println("circularMenuPane parent is null, cannot remove.");
    }

    circularMenuPane.getChildren().clear();
    circularMenuPane.setVisible(false);
    circularMenuPane.setManaged(false);

    // Ensure the UI is updated
    circularMenuPane.getScene().getWindow().sizeToScene();
    System.out.println("Menu hidden and pane removed from parent");
}`
```