To reproduce:
1) start an app below;
2) move mouse cursor to the second menu;
3) press ALT key twice;
4) click mouse button
Both the second and the first menu buttons will be selected unexpectedly.

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.*;
import javafx.scene.layout.HBox;
import javafx.stage.Stage;

public class App extends Application {

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

    @Override
    public void start(Stage stage) throws Exception {
        MenuBar control = new MenuBar();
        for (int i = 0; i < 5; i++) {
            Menu m = new Menu("Menu " + String.valueOf(i + 1));
            for (int j = 0; j < 5; j++) {
                m.getItems().add(new MenuItem("Item " + String.valueOf(j + 1)));
            }
            control.getMenus().add(m);
        }
        Scene scene = new Scene(new HBox(control));
        stage.setScene(scene);
        stage.show();
    }
}