Hi Tony,
Is your menu an include on a .php page, or is it on an html page?
Is there a link to your page on -line?
Are you still unable to see the javascript? Try looking at the menu.php page directly (there should be a link to it in your page) :
Edit: Deleted
In your preferences, under 'Invisible Elements', at the bottom - is the 'Server-Side Includes: Show contents of included file' checked? If not, check that too.
Sorry, I'm an idiot. The path to your php page is in your include. Ignore the css link above.
<?php require_once("CSSMenuWriter/cssmw/menu.php"); ?>