OK - its nothing to do with Easy Populate - its to do with your configure.php
in this line
define('DIR_FS_DOCUMENT_ROOT', '/home/user/www/public_html/'); // where the pages are located on the server
I had it pointing to my oscommerce install like this
define('DIR_FS_DOCUMENT_ROOT', '/home/user/www/public_html/catalog/'); // where the pages are located on the server
whereas it should have been as the top line - pointing to my document root only.
It worked for me :)