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 :
Windows 7, professional, 64 bit

A DESCRIPTION OF THE PROBLEM :
If the scene is set on the stage AFTER it is shown it is not sized correctly. 

(Background: This was discovered during unit testing with the testFX framework which reuses the same stage for multiple tests with different scenes).

This appears to be a regression. The same code running on Java 8u144 works as expected.

REGRESSION.  Last worked in version 8u151

ADDITIONAL REGRESSION INFORMATION: 
java version "1.8.0_144"
Java(TM) SE Runtime Environment (build 1.8.0_144-b01)
Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the test case

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
StackPane should fill the window exactly, i.e. the red border should sit just inside the Stage.
ACTUAL -
StackPane appears larger that the stage.
If you resize the stage manually then the StackPane adjusts and is rendered correctly.

REPRODUCIBILITY :
This bug can be reproduced often.

---------- BEGIN SOURCE ----------
import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.Label;
import javafx.scene.layout.StackPane;
import javafx.stage.Stage;

public class SceneSizeIssue extends Application {

    public static void main(String[] args) {
        launch(args);
    }

    @Override
    public void start(Stage stage) throws Exception {
        stage.setX(50);
        stage.setY(50);
        stage.setWidth(400);
        stage.setHeight(300);

        stage.show();

        StackPane box = new StackPane(new Label("Rigby"));
        box.setStyle("-fx-border-color: red");
        stage.setScene(new Scene(box));

    }

}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Hide the stage and then show it again