If a popup window stays open as the result of
previous action, next menu pushing fails. Exactly
said, it only closes the popup but it does nothing
else.
Try following:

        JemmyProperties.setCurrentDispatchingModel(
              
JemmyProperties.getCurrentDispatchingModel() |  
               JemmyProperties.SHORTCUT_MODEL_MASK);
        
        JFrameOperator frame = new
JFrameOperator("NetBeans");
        JMenuBarOperator menu = new
JMenuBarOperator(frame);
        menu.showMenuItem("File|Save All", "|");
        
        menu.pushMenuNoBlock("Project|Project
Manager", "|");
        
        System.out.println("\n\nFinished.");