Code:
/ * DIR_FS_* = Filesystem directories (local/physical)
//the following path is a COMPLETE path to your Zen Cart files. eg: /var/www/vhost/accountname/public_html/store/
define('DIR_FS_CATALOG', '/home/mysite/public_html/store2/');
define('DIR_FS_DOWNLOAD', DIR_FS_CATALOG . 'download/');
define('DIR_FS_DOWNLOAD_PUBLIC', DIR_FS_CATALOG . 'pub/');
define('DIR_WS_UPLOADS', DIR_WS_IMAGES . 'uploads/');
define('DIR_FS_UPLOADS', DIR_FS_CATALOG . DIR_WS_UPLOADS);
define('DIR_FS_EMAIL_TEMPLATES', DIR_FS_CATALOG . 'email/');
Above is an extract from my own configure.php file for mydomain.com/store2
.. as you can see the download folder is set exactly as I stated in my initial post to your query...