This is enough to show the problem:

public void start(Stage primaryStage) throws Exception {
    primaryStage.setScene(new Scene(createContent()));
    primaryStage.show();
}

public Parent createContent() {
    Region r = new Region();
    r.setPrefSize(30.5, 30);
    BackgroundFill bf1 = new BackgroundFill(Color.BLACK, null, null);
    r.setBackground(new Background(bf1, bf1));//adding the same fill twice to enable caching
    r.setLayoutX(10);
    r.setLayoutY(10);
    return new Pane(r);
}

Note the last column in the region should be gray, but is pure black (in fact, the last column is not rendered).
change
r.setBackground(new Background(bf1, bf1));
to
r.setBackground(new Background(bf1));
will disable region cache and result in correct rendering.