I'm running on javafx.runtime.version=8.0.0-ea-b103

With this simple application :

@Override
    public void start(Stage primaryStage) throws Exception {
        BorderPane borderPane = new BorderPane();

        ToolBar toolbar = new ToolBar();

        Button button = new Button("Test");
        button.setId("mybutton");
        toolbar.getItems().add(button);

        //borderPane.setCenter(button);
        borderPane.setTop(toolbar);
        System.out.println("MyButton = " + borderPane.lookupAll("#mybutton"));

        Scene scene = new Scene(borderPane, 1024, 768);
        primaryStage.setScene(scene);
        primaryStage.show();
        System.out.println("MyButton = " + borderPane.lookupAll("#mybutton"));};
}

When the button is inside a toolbar, the first lookupAll return an empty set.
The second lookup work.

When the button is directly in the border pane, all lookup work.