The menu in your first screen shot should be represented by the php icon in the top navigation area. What you are seeing on the menu.php page is correct.
Where the menu should be on the template you should have an include file reference. Sometimes when you are applying to a template the paths can get messed up. Check the path of this include to ensure that it is pointing to the resource correctly. Also check the other links on the page that are going to the CSSMenuWriter folder.
When you test the pages out that are derived from this template do they have the menu present?