Run this program :
"
import javafx.application.Application;
import static javafx.application.Application.launch;
import javafx.geometry.Orientation;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.MenuButton;
import javafx.scene.control.Separator;
import javafx.scene.control.ToolBar;
import javafx.scene.layout.HBox;
import javafx.stage.Stage;

/*
 * Copyright NellArmonia 2014
 */
public class testToolBar extends Application {

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

    @Override
    public void start(Stage primaryStage) throws Exception {
        ToolBar bar = new ToolBar();
        HBox box = new HBox(getButton(), getMenuButton(), new Separator(Orientation.VERTICAL), getButton(), getMenuButton(), getMenuButton());
        HBox box2 = new HBox(getButton(), getMenuButton(), new Separator(Orientation.VERTICAL), getButton(), getMenuButton(), getMenuButton());
        bar.getItems().addAll(box, box2);

        Scene scene = new Scene(bar);
        primaryStage.setScene(scene);
        primaryStage.setMinHeight(300);
        primaryStage.setMinWidth(100);
        primaryStage.show();
    }

    private Button getButton() {
        return new Button("b");
    }

    private MenuButton getMenuButton() {
        return new MenuButton("t");
    }
}
"

Click on the right edge of the window and resize the window. You will see that we have a flicker because the separator are disapearing somehow.

Tested on JDK 8u40 b12