Does it fail to show in your 'Files' panel in Dreamweaver (local view), in your 'Files' panel in (remote view), or both?
If it shows in your files panel in 'local view' but not in 'remote view', then check that you have the right Host Directory defined in your remote info in your site definition. (see pic). You would need to check what your particular 'host directory' is.
Another thing to try: Create a new site via 'manage sites'. Run cssmenuwriter on a new page. Do you get both directories to show up there?