FULL PRODUCT VERSION :
java version "9.0.4"
Java(TM) SE Runtime Environment (build 9.0.4+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.4+11, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 10.0.16299.192]

A DESCRIPTION OF THE PROBLEM :
Adding a Shape node to a Pane root in the start method of a JavaFX application, the JavaFX application window is presented with the Shape drawn as expected, but shortly after a NPE is generated.

This occurs if passing the object to the Pane constructor, or if adding to the Pane object later with a root.getChildren().add(...) call.

The NPE is generated, but the window seems to be drawn correctly.

This is happening for multiple different Shape objects, but not a Text object.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
In a simple JavaFX application's start method:

- create a Rectangle object
- create a Pane object containing this rectangle
- create a Scene object containing this Pane
- update the stage with this Scene object
- wait briefly

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
I was expecting the window and its children to be drawn without an exception.
ACTUAL -
A NPE is produced for each Shape object added to the Pane.

ERROR MESSAGES/STACK TRACES THAT OCCUR :
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
at javafx.graphics/com.sun.glass.ui.win.WinAccessible.getUnignoredChildren(Unknown Source)
at javafx.graphics/com.sun.glass.ui.win.WinAccessible.Navigate(Unknown Source)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
package drawing;

import javafx.application.*;
import javafx.scene.*;
import javafx.scene.layout.*;
import javafx.scene.paint.*;
import javafx.scene.shape.*;
import javafx.scene.text.*;
import javafx.stage.*;

public class DrawBug extends Application
{
    private Scene scene;
    private Pane root;
    
    public void start(Stage stage)
    {
        Rectangle rect = new Rectangle(0, 0, 300, 200);
        rect.setFill(Color.LIGHTGRAY);

        Text text = new Text(50, 50, "Hello");
        
        root = new Pane();
        root.getChildren().addAll(rect, text);
        // NOTE: Bug also happens with root = new Pane(rect, text);

        root.setPrefSize(400, 300);
        scene = new Scene(root);
        stage.setScene(scene);
        stage.show();
    }
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
package drawing;

import javafx.application.*;
import javafx.scene.*;
import javafx.scene.layout.*;
import javafx.scene.paint.*;
import javafx.scene.shape.*;
import javafx.scene.text.*;
import javafx.stage.*;

public class DrawBugAvoided extends Application
{
    private Scene scene;
    private Pane root;
    
    public void start(Stage stage)
    {
        Rectangle rect = new Rectangle(0, 0, 300, 200);
        rect.setFill(Color.LIGHTGRAY);

        Text text = new Text(50, 50, "Hello");
        
        root = new Pane();

        // Adding Shapes outside of the start method mostly works.
        // Though if you do move the mouse quickly onto the region of
        // the window that has the filled rectangle, it still generates the
        // NPE.
        root.setOnMouseEntered(event ->
        {
            if (root.getChildren().size() == 0)
                root.getChildren().addAll(rect, text);
        });

        root.setPrefSize(400, 300);
        scene = new Scene(root);
        stage.setScene(scene);
        stage.show();
    }
}