Finally found it - Long story short there was an issue in my configure.php file. When I moved from a subdomain to a primary domain, my subdirectory redirection wasn't working the same (no wildcards on the primary domain).
This meant changing my server and directory definitions, where subdir is a parent directory to the catalog.
Code:
define('HTTP_SERVER', 'http://www.domainname.com/subdir');
define('HTTPS_SERVER', 'https://secure.bluehost.com/~myname/subdir');
define('HTTP_CATALOG_SERVER', 'http://www.domainname.com/subdir');
define('HTTPS_CATALOG_SERVER', 'https://secure.bluehost.com/~myname/subdir');
define('DIR_WS_ADMIN', '/zencartdirectory/admin/');
define('DIR_WS_CATALOG', '/zencartdirectory/');