> httrack is not downloading files that use full paths
> for css and js files. (IE: <script
> src=http://www.test.com/js/test.js
> type="text/javascript"></script> )

<http://www.test.com/js/test.js> does not exist (404) and you didn't give the
page url.

I'd guess that the sites don't match and you don't have Get non-html checked
nor specifically allowing +*.js. 

Or it's the same site, no non-html, no +*.js and Direction=down only.

Or the site's robots.txt prevents /js