Secondary scene returns incorrect coordinates.
The sample below returns something like

x: 974.5
y: 369.33334362506866
x: 65.0
y: 24.0

At the same an actual window position is correct.

import javafx.application.Application;
import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.Label;
import javafx.stage.Modality;
import javafx.stage.Stage;
import javafx.stage.WindowEvent;

public class App extends Application {
    public static void main(String[] args) {
        launch(args);
    }

    public void start(Stage primaryStage) {

        class MyDialog extends Stage {

            public MyDialog(Stage parent) {
// initOwner(parent);
// initModality(Modality.WINDOW_MODAL);
                setScene(new Scene(new Label("Label")));
                sizeToScene();
            }
        }

        Button button = new Button("Show Dialog");
        button.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent event) {
                final Stage dlg = new MyDialog(primaryStage);
                dlg.xProperty().addListener(new ChangeListener<Number>() {
                    @Override
                    public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
                        System.out.println("x: " + newValue);
                    }
                });
                dlg.yProperty().addListener(new ChangeListener<Number>() {
                    @Override
                    public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
                        System.out.println("y: " + newValue);
                    }
                });
                dlg.showAndWait();
            }
        });

        primaryStage.setScene(new Scene(button));
        primaryStage.show();
    }

}