// ...
public class MclViewerFrame extends JFrame {
// ...
private MainMenuBar mainMenuBar = null;
// ...
this.mainMenuBar = new MainMenuBar(this);
// WindowBuilder doesn't work with this line
this.setJMenuBar(this.mainMenuBar);

// ...
public class MainMenuBar extends JMenuBar {
// ...

import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowEvent;

import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;

public class TestMenuBar extends JMenuBar {

	private static final long serialVersionUID = 1L;
	private String strFile = "File";
	private String strClose = "Close";
	
	private TestFrame parent = null;
	
	private JMenu menuFile = new JMenu(this.strFile);
	
	public TestMenuBar(TestFrame parent) {
		this.parent = parent;
		setMenuFile();
	}
	
	private void setMenuFile() {
		
		this.menuFile.add(setMenuItemFileClose());
		this.add(this.menuFile);
	}
	
	private JMenuItem setMenuItemFileClose() {
		
		// exit
		JMenuItem menu = new JMenuItem();
		menu.setText(this.strClose);
		menu.addActionListener(new ActionListener() {
			public void actionPerformed(ActionEvent e) {
				parent.processWindowEvent(new WindowEvent(parent, WindowEvent.WINDOW_CLOSING));
			}
		});
		return menu;
	}
}

import java.awt.Dimension;

public class TestFrame extends JFrame{

	private TestMenuBar testMenuBar = null;
	public static final String TITLE = "Test WindowBuilder";
	
	public TestFrame() {
		
		init();
	}
	
	private void init() {
		
		setTitle(TITLE);
		
		testMenuBar = new TestMenuBar(this);
		setJMenuBar(testMenuBar);
		
		setMinimumSize(new Dimension(800, 600));
		setVisible(true);
		setExtendedState(getExtendedState() | MAXIMIZED_BOTH);
	}
	
	protected void processWindowEvent(WindowEvent e) {
		
		if (e.getID() == WindowEvent.WINDOW_CLOSING) {

			// close
			this.setVisible(false);
			this.dispose();
			System.exit(0);
		}
		super.processWindowEvent(e);
	}
}

public class Main {
	
	private static TestFrame testFrame = null;

	/**
	 * @param args
	 */
	public static void main(String[] args) {

		testFrame = new TestFrame();

	}

}

java.lang.ClassCastException: javax.swing.JPanel cannot be cast to javax.swing.JMenuBar
	at org.eclipse.wb.internal.swing.model.component.menu.JMenuBarInfo.refresh_afterCreate(JMenuBarInfo.java:100)
	at org.eclipse.wb.core.model.ObjectInfo.refresh_afterCreate(ObjectInfo.java:621)
	at org.eclipse.wb.core.model.JavaInfo.refresh_afterCreate(JavaInfo.java:1217)
	at org.eclipse.wb.core.model.AbstractComponentInfo.refresh_afterCreate(AbstractComponentInfo.java:238)
	at org.eclipse.wb.core.model.ObjectInfo.refreshCreate0(ObjectInfo.java:552)
	at org.eclipse.wb.core.model.ObjectInfo.access$0(ObjectInfo.java:546)
	at org.eclipse.wb.core.model.ObjectInfo$5$1.run(ObjectInfo.java:486)
	at org.eclipse.wb.internal.core.utils.execution.ExecutionUtils.runDesignTime(ExecutionUtils.java:139)
	at org.eclipse.wb.core.model.ObjectInfo$5.run(ObjectInfo.java:484)
	at org.eclipse.wb.internal.swing.utils.SwingUtils$2.run(SwingUtils.java:76)
	at java.awt.event.InvocationEvent.dispatch(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$000(Unknown Source)
	at java.awt.EventQueue$1.run(Unknown Source)
	at java.awt.EventQueue$1.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)