Program: 96252
Project: 96252
Buggy source:
public _AppIndicatorTray(final SystemTray systemTray){
  super();
  Gtk.startGui();
  Gtk.dispatch(new Runnable(){
    @Override public void run(){
      File image=ImageUtils.getTransparentImage(ImageUtils.ENTRY_SIZE);
      String id=System.nanoTime() + "String_Node_Str";
      appIndicator=AppIndicator.app_indicator_new(id,image.getAbsolutePath(),AppIndicator.CATEGORY_APPLICATION_STATUS);
      createAppIndicatorMenu();
    }
  }
);
  Gtk.waitForStartup();
  SwingUtil.invokeLater(new Runnable(){
    @Override public void run(){
      final SwingMenu swingMenu=new SwingMenu(null){
        @Override public void setEnabled(        final MenuItem menuItem){
          Gtk.dispatch(new Runnable(){
            @Override public void run(){
              boolean enabled=menuItem.getEnabled();
              if (visible && !enabled) {
                AppIndicator.app_indicator_set_status(appIndicator,AppIndicator.STATUS_PASSIVE);
                visible=false;
              }
 else               if (!visible && enabled) {
                AppIndicator.app_indicator_set_status(appIndicator,AppIndicator.STATUS_ACTIVE);
                visible=true;
              }
            }
          }
);
        }
        @Override public void setImage(        final MenuItem menuItem){
          imageFile=menuItem.getImage();
          if (imageFile == null) {
            return;
          }
          Gtk.dispatch(new Runnable(){
            @Override public void run(){
              AppIndicator.app_indicator_set_icon(appIndicator,imageFile.getAbsolutePath());
              if (!isActive) {
                isActive=true;
                AppIndicator.app_indicator_set_status(appIndicator,AppIndicator.STATUS_ACTIVE);
                hookMenuOpen();
              }
            }
          }
);
          SwingUtil.invokeLater(new Runnable(){
            @Override public void run(){
              ((TrayPopup)_native).setTitleBarImage(imageFile);
            }
          }
);
        }
        @Override public void setText(        final MenuItem menuItem){
        }
        @Override public void setShortcut(        final MenuItem menuItem){
        }
        @Override public void remove(){
          if (!shuttingDown.getAndSet(true)) {
            final AppIndicatorInstanceStruct savedAppIndicator=appIndicator;
            appIndicator=null;
            Gtk.dispatch(new Runnable(){
              @Override public void run(){
                AppIndicator.app_indicator_set_status(savedAppIndicator,AppIndicator.STATUS_PASSIVE);
                Pointer p=savedAppIndicator.getPointer();
                Gobject.g_object_unref(p);
              }
            }
);
            Gtk.shutdownGui();
            super.remove();
          }
        }
      }
;
      TrayPopup popupMenu=(TrayPopup)swingMenu._native;
      popupMenu.pack();
      popupMenu.setFocusable(true);
      popupMenu.setOnHideRunnable(new Runnable(){
        @Override public void run(){
          if (appIndicator == null) {
            return;
          }
          Gtk.dispatchAndWait(new Runnable(){
            @Override public void run(){
              createAppIndicatorMenu();
              hookMenuOpen();
            }
          }
);
        }
      }
);
      popupRunnable=new Runnable(){
        @Override public void run(){
          Point point=MouseInfo.getPointerInfo().getLocation();
          TrayPopup popupMenu=(TrayPopup)swingMenu._native;
          popupMenu.doShow(point,SystemTray.DEFAULT_TRAY_SIZE);
        }
      }
;
      bind(swingMenu,null,systemTray);
    }
  }
);
  if (System.getProperty("String_Node_Str","String_Node_Str").equals("String_Node_Str")) {
    Gtk.dispatch(new Runnable(){
      @Override public void run(){
        AppIndicator.app_indicator_set_status(appIndicator,AppIndicator.STATUS_ACTIVE);
        AppIndicator.app_indicator_set_title(appIndicator,"String_Node_Str");
      }
    }
);
  }
}

Fixed version (ground truth):
public _AppIndicatorTray(final SystemTray systemTray){
  super();
  Gtk.startGui();
  Gtk.dispatch(new Runnable(){
    @Override public void run(){
      File image=ImageUtils.getTransparentImage(ImageUtils.ENTRY_SIZE);
      String id=System.nanoTime() + "String_Node_Str";
      appIndicator=AppIndicator.app_indicator_new(id,image.getAbsolutePath(),AppIndicator.CATEGORY_APPLICATION_STATUS);
      createAppIndicatorMenu();
    }
  }
);
  Gtk.waitForStartup();
  SwingUtil.invokeLater(new Runnable(){
    @Override public void run(){
      final SwingMenu swingMenu=new SwingMenu(null){
        @Override public void setEnabled(        final MenuItem menuItem){
          Gtk.dispatch(new Runnable(){
            @Override public void run(){
              boolean enabled=menuItem.getEnabled();
              if (visible && !enabled) {
                AppIndicator.app_indicator_set_status(appIndicator,AppIndicator.STATUS_PASSIVE);
                visible=false;
              }
 else               if (!visible && enabled) {
                AppIndicator.app_indicator_set_status(appIndicator,AppIndicator.STATUS_ACTIVE);
                visible=true;
              }
            }
          }
);
        }
        @Override public void setImage(        final MenuItem menuItem){
          imageFile=menuItem.getImage();
          if (imageFile == null) {
            return;
          }
          Gtk.dispatch(new Runnable(){
            @Override public void run(){
              AppIndicator.app_indicator_set_icon(appIndicator,imageFile.getAbsolutePath());
              if (!isActive) {
                isActive=true;
                AppIndicator.app_indicator_set_status(appIndicator,AppIndicator.STATUS_ACTIVE);
                hookMenuOpen();
              }
            }
          }
);
          SwingUtil.invokeLater(new Runnable(){
            @Override public void run(){
              ((TrayPopup)_native).setTitleBarImage(imageFile);
            }
          }
);
        }
        @Override public void setText(        final MenuItem menuItem){
        }
        @Override public void setShortcut(        final MenuItem menuItem){
        }
        @Override public void remove(){
          if (!shuttingDown.getAndSet(true)) {
            final AppIndicatorInstanceStruct savedAppIndicator=appIndicator;
            appIndicator=null;
            Gtk.dispatch(new Runnable(){
              @Override public void run(){
                AppIndicator.app_indicator_set_status(savedAppIndicator,AppIndicator.STATUS_PASSIVE);
                Pointer p=savedAppIndicator.getPointer();
                Gobject.g_object_unref(p);
              }
            }
);
            Gtk.shutdownGui();
            super.remove();
          }
        }
      }
;
      TrayPopup popupMenu=(TrayPopup)swingMenu._native;
      popupMenu.pack();
      popupMenu.setFocusable(true);
      popupMenu.setOnHideRunnable(new Runnable(){
        @Override public void run(){
          if (appIndicator == null) {
            return;
          }
          Gtk.dispatchAndWait(new Runnable(){
            @Override public void run(){
              createAppIndicatorMenu();
              hookMenuOpen();
            }
          }
);
        }
      }
);
      popupRunnable=new Runnable(){
        @Override public void run(){
          Point point=MouseInfo.getPointerInfo().getLocation();
          TrayPopup popupMenu=(TrayPopup)swingMenu._native;
          popupMenu.doShow(point,SystemTray.DEFAULT_TRAY_SIZE);
        }
      }
;
      bind(swingMenu,null,systemTray);
    }
  }
);
}