I did a test using your nickusborne template and then creating a site sculptor design, and i was not able to reproduce the issue you are seeing. Looking at the sitesculptor template file you have sent me, it looks like it is including all the css and js files for the menu, but it does not have the menu file:
<?php require_once("../CSSMenuWriter/cssmw_content/menu.php"); ?>
However, looking more at your template, i see that you have menu id specified more than once in your template:
the id should be unique and can't be used more than once. That could be causing the confusion. Try having just one <div id="menu"> on your page to see if that resolves the issue.