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?
What resource should the path of the "include" point to?
Yes, the menu came with the template. The template was created by Site Assist Pro. My take is there maybe some conflict between Site Assist Pro and CSS Menu Writer.