Had to change "spacing" property to a new value then back to old value on VBox to refresh the view when updating the height of a single node within that VBox.
Below codes can be used to re-produce the problem

import javafx.stage.Stage;
import javafx.scene.Scene;
import javafx.scene.shape.Rectangle;
import javafx.scene.paint.Color;
import javafx.scene.layout.VBox;
import javafx.scene.input.MouseEvent;

var vBox: VBox;
var vRect1: Rectangle;
var vRect2: Rectangle;

Stage {
    title: "VBox"
    width: 600
    height: 600
    visible: true

    scene: Scene{
            content: [
                vBox = VBox {
                    spacing: 10
                    content: [
                        vRect1 = Rectangle {
                            x: 10
                            y: 10
                            width:200
                            height:25
                            stroke: Color.BLACK
                            fill: Color.GREEN
                        }//Rectangle

                        vRect2 = Rectangle {
                            x: 10
                            y: 10
                            width:200
                            height:25
                            stroke: Color.BLACK
                            fill: Color.BLUE
                        }//Rectangle
                    ]
                    onMousePressed: function(e: MouseEvent) {
                        vRect1.height++;
                        // vBox.spacing++; // The workaround is to uncomment this line, and
                        // vBox.spacing--; // this line
                    }
                }
           ]
        } //Scene
}//Stage