Run the code :

    @Override
    public void start(Stage stage) throws Exception {
        RadioButton b1 = new RadioButton("Text");
        b1.setGraphic(new Rectangle(10, 10));
        b1.setStyle("-fx-border-color: BLACK;");
        b1.setAlignment(Pos.CENTER_RIGHT);
        b1.setPrefSize(150, 60);

        CheckBox b2 = new CheckBox("Text");
        b2.setGraphic(new Rectangle(10, 10));
        b2.setStyle("-fx-border-color: BLACK;");
        b2.setAlignment(Pos.CENTER_RIGHT);
        b2.setPrefSize(150, 60);

        VBox pane = new VBox();
        pane.getChildren().addAll(b1, b2);
        pane.setMinSize(200, 200);
        pane.setAlignment(Pos.CENTER);

        stage.setScene(new Scene(pane));
        stage.show();
    }

Command setAlignment is ignored for radioButton and CheckBox.
(it is not ignored for other labeled controls, as I saw)

If you change setPrefSize() on setMinSize(), then it will work.