HMWP is compatible with almost all premium themes. Genesis was also tested before so your problem is not related to your theme.
You just need to follow quick guide fix. Also, make sure you don’t use several themes at the same time (e.g. maintenance plugins, one theme for each pages and so on)
If your problem persists please provide more details (URL + htaccess file content)
HMWP is not an anti-spam plugin but it’s still useful for blocking some type of spammers. Try enabling ‘Avoid direct access to PHP files’ plus changing ‘wp_comments_post.php’ URL.