原来是设置了这个导致的

configurer.setSaveAndRestore(true);
代码如下:

import org.eclipse.jface.action.Action;
import org.eclipse.jface.action.IMenuManager;
import org.eclipse.jface.action.MenuManager;
import org.eclipse.swt.SWT;
import org.eclipse.swt.events.ShellAdapter;
import org.eclipse.swt.events.ShellEvent;
import org.eclipse.swt.widgets.Event;
import org.eclipse.swt.widgets.Listener;
import org.eclipse.swt.widgets.Menu;
import org.eclipse.swt.widgets.Shell;
import org.eclipse.swt.widgets.Tray;
import org.eclipse.swt.widgets.TrayItem;
import org.eclipse.ui.IWorkbenchWindow;
import org.eclipse.ui.PlatformUI;
import org.eclipse.ui.plugin.AbstractUIPlugin;

public class HookSysTray {

 private TrayItem trayItem;
 
 public HookSysTray() {
  
 }
 
 public void createSysTray(final IWorkbenchWindow window) {
  trayItem = initTrayItem(window);
  if(trayItem != null) {
   trayPopupMenu(window);
   trayMinimize(window);
  }
 }
 //最小化到颖P
 private void trayMinimize(final IWorkbenchWindow window) {
  // TODO Auto-generated method stub
  window.getShell().addShellListener(new ShellAdapter(){

   @Override
   public void shellIconified(ShellEvent e) {
    // TODO Auto-generated method stub
    window.getShell().setVisible(false);
   }
   
  });
  trayItem.addListener(SWT.Selection, new Listener(){

   public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    Shell shell = window.getShell();
    if(!shell.isVisible()) {
     shell.setVisible(true);
     window.getShell().setMinimized(false);
    }
   }
   
  });
 }
 //颖P出菜?
 private void trayPopupMenu(final IWorkbenchWindow window) {
  // TODO Auto-generated method stub
  trayItem.addListener(SWT.MenuDetect, new Listener() {

   public void handleEvent(Event event) {
    // TODO Auto-generated method stub
    MenuManager trayMenu = new MenuManager();
    Menu menu = trayMenu.createContextMenu(window.getShell());
    fillTrayItem(trayMenu, window);
    menu.setVisible(true);
   }
  });
 }

 //造颖P菜雾
 private void fillTrayItem(IMenuManager trayMenu, final IWorkbenchWindow window) {
  Action exitSystem = new Action("退出系統[&E]",
AbstractUIPlugin.imageDescriptorFromPlugin(
    IAppConstants.APPLICATION_ID, IImagekey.EXIT_STSTEN)) {

     @Override
     public void run() {
      // TODO Auto-generated method stub
      PlatformUI.getWorkbench().close();
     }
   
  };
  trayMenu.add(exitSystem);
 }
 //初始化
 private TrayItem initTrayItem(IWorkbenchWindow window) {
  // TODO Auto-generated method stub
  final Tray tray = window.getShell().getDisplay().getSystemTray();
  if(tray == null)
   return null;
  trayItem = new TrayItem(tray, SWT.NONE);
  trayItem.setImage(CacheImage.getInstance().getImage(
    IAppConstants.APPLICATION_ID, IImagekey.WINDOW_IMAGE));
  trayItem.setToolTipText(IAppConstants.APPLICATION_TITLE);
  return trayItem;
 }
 
 //最小化程式窗口
 public void windowMinimized(final Shell shell) {
  shell.setMinimized(true);
  shell.setVisible(false);
 }
 
 //
 public void disponse() {
  if(trayItem != null)
   trayItem.dispose();
 }
}

import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;

import org.eclipse.swt.graphics.Image;
import org.eclipse.ui.plugin.AbstractUIPlugin;

public class CacheImage {

 private final Map<String, Image> imageMap = new HashMap<String, Image>();
 private static CacheImage INSTANCE = null;
 
 private CacheImage(){
  
 }
 //單例
 public static CacheImage getInstance() {
  if(INSTANCE == null)
   INSTANCE = new CacheImage();
  return INSTANCE;
 }
 //獲得圖片
 public Image getImage(String applicationId, String imageName) {
  if(imageName == null)
   return null;
  Image image = imageMap.get(imageName);
  if(image == null) {
   image = AbstractUIPlugin.imageDescriptorFromPlugin(applicationId,
imageName).createImage();//應用程序的ID，圖片的路徑
   imageMap.put(imageName, image);
  }
  return image;
 }
 //dispose資源
 public void dispose() {
  Iterator<Image> iterator = imageMap.values().iterator();
  while(iterator.hasNext())
   iterator.next().dispose();
  imageMap.clear();
 }
}

import org.eclipse.jface.action.Action;
import org.eclipse.jface.dialogs.ErrorDialog;
import org.eclipse.ui.IWorkbenchPage;
import org.eclipse.ui.IWorkbenchWindow;
import org.eclipse.ui.PartInitException;
import org.eclipse.ui.actions.ActionFactory.IWorkbenchAction;
import org.eclipse.ui.views.IViewDescriptor;

public class ShowViewAction extends Action implements IWorkbenchAction {

 private IWorkbenchWindow workbenchWindow;
 private IViewDescriptor desc;
 
 public ShowViewAction(IWorkbenchWindow window, IViewDescriptor desc) {
  super("");
  /** 获得视图的名称 */
  String label = desc.getLabel();
  /** 设置操作的名称 */
  setText(label);
  /** 设置操作的图标为视图的图标 */
  setImageDescriptor(desc.getImageDescriptor());
  /** 设置操作的提示文本 */
  setToolTipText(label);
  setId("ShowView" + desc.getId());
  
  this.workbenchWindow = window;
  this.desc = desc;
 }
 
 @Override
 public void run() {
  /** 获得当前工作区及获得工作页面 */
  IWorkbenchPage page = workbenchWindow.getActivePage();
  /** 如果页面不为null */
  if (page != null) {
   try {
    /** 显示视图 */
    page.showView(desc.getId());
   } catch (PartInitException e) {
    ErrorDialog.openError(workbenchWindow.getShell(), "打开视图错误
！", e.getMessage(), e.getStatus());
   }
  }
 }

 @Override
 public void dispose() {
  
  workbenchWindow = null;
 }

}

import org.eclipse.ui.IWorkbenchWindow;
import org.eclipse.ui.actions.ActionFactory.IWorkbenchAction;
import org.eclipse.ui.views.IViewDescriptor;

public class ActionManager {

 public static IWorkbenchAction createHelloWorldAction(IWorkbenchWindow window) {
  if(window == null)
   throw new IllegalArgumentException();
  IWorkbenchAction helloWorldAction = new HelloWorldAction(window);
  return helloWorldAction;
 }
 
 /**获得plugin.xml文件中配置的视图信息*/
 public static IWorkbenchAction createShowViewAction(IWorkbenchWindow window, String viewId) {
  if(window == null)
   throw new IllegalArgumentException();
  IViewDescriptor desc = window.getWorkbench().getViewRegistry().find(viewId);
  IWorkbenchAction action = new ShowViewAction(window, desc);
  return action;
 }
}

import org.eclipse.jface.action.MenuManager;
import org.eclipse.swt.SWT;
import org.eclipse.swt.graphics.Image;
import org.eclipse.swt.graphics.Point;
import org.eclipse.swt.graphics.Rectangle;
import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Event;
import org.eclipse.swt.widgets.Listener;
import org.eclipse.swt.widgets.Menu;
import org.eclipse.swt.widgets.Shell;
import org.eclipse.swt.widgets.Tray;
import org.eclipse.swt.widgets.TrayItem;
import org.eclipse.ui.IWorkbenchWindow;
import org.eclipse.ui.application.ActionBarAdvisor;
import org.eclipse.ui.application.IActionBarConfigurer;
import org.eclipse.ui.application.IWorkbenchWindowConfigurer;
import org.eclipse.ui.application.WorkbenchWindowAdvisor;

public class ApplicationWorkbenchWindowAdvisor extends WorkbenchWindowAdvisor {

 private TrayItem trayItem;//系统托盘对象
 private Image trayImage;//系统托盘图标对象
 /** 程序的菜单条 */
 private ApplicationActionBarAdvisor actionBarAdvisor;
 
    public ApplicationWorkbenchWindowAdvisor(IWorkbenchWindowConfigurer configurer) {
        super(configurer);
    }
    /** 创建菜单条对象 */
    public ActionBarAdvisor createActionBarAdvisor(IActionBarConfigurer configurer) {
        actionBarAdvisor = new ApplicationActionBarAdvisor(configurer);
     return actionBarAdvisor;
    }
   
    /** 打开窗口前调用该方法，对窗口初始化设置 */
    public void preWindowOpen() {
        IWorkbenchWindowConfigurer configurer = getWindowConfigurer();
        configurer.setInitialSize(new Point(600, 400));
        configurer.setShowCoolBar(true);//工具栏
        configurer.setShowStatusLine(false);//状态栏
       
        configurer.setShowPerspectiveBar(true);//透视图
        configurer.setShowProgressIndicator(true);//进度条
       
        final IWorkbenchWindow window = super.getWindowConfigurer().getWindow();
        /** 创建系统托盘 */
        trayItem = initTrayItem(window);
        /** 如果支持系统托盘，则创建托盘的菜单 */
        if(trayItem != null) {
         createPopupMenu(window);
        }
    }
   
    /**
  * 创建系统托盘菜单
  *
  * @param window
  *            工作台窗口对象
  */
    private void createPopupMenu(final IWorkbenchWindow window) {
  trayItem.addListener(SWT.MenuDetect, new Listener() {

   @Override
   public void handleEvent(Event event) {
    MenuManager trayMenu = new MenuManager();
    Menu menu = trayMenu.createContextMenu(window.getShell());
    /**
     * 调用fillTrayItem方法创建系统托盘对象，可以直接利用菜单栏中的操作 而不需要，重新创建操作
     */
    actionBarAdvisor.fillTrayItem(trayMenu);
    menu.setVisible(true);
   }
   
  });
  
 }

 /**
  * 初始化系统托盘对象
  *
  * @param window
  *            工作台窗口对象
  * @return 该程序所对应的系统托盘对象
  */
 private TrayItem initTrayItem(IWorkbenchWindow window) {
  final Tray tray = Display.getCurrent().getSystemTray();
  if(tray == null)
   return null;
  TrayItem trayItem = new TrayItem(tray, SWT.NONE);
  trayImage = Activator.getImageDescriptor("icons/logo.gif").createImage();
  trayItem.setImage(trayImage);
  trayItem.setToolTipText("System Tray");
  
  return trayItem;
 }

 @Override
 public void postWindowOpen() {
  //窗口居中显示
  Shell shell = getWindowConfigurer().getWindow().getShell();
  Rectangle screenSize = Display.getDefault().getClientArea();
  Rectangle frameSize = shell.getBounds();
  shell.setLocation((screenSize.width - frameSize.width)/2, (screenSize.height - frameSize.height)/2);
 }
   
 /** 释放窗口，释放系统托盘 */
 public void dispose() {
  if (trayImage != null) {
   trayImage.dispose();
   trayItem.dispose();
  }
 }

}