Could you please add this in your core next time? as descrived here: http://wpdailybits.com/blog/notify-post-author-for-new-comment-disqus/45
From:
$comment_id = $commentdata['comment_ID'];
update_comment_meta($comment_id, 'dsq_parent_post_id', $comment->parent_post);
update_comment_meta($comment_id, 'dsq_post_id', $comment->id);
To:
$comment_id = $commentdata['comment_ID'];
update_comment_meta($comment_id, 'dsq_parent_post_id', $comment->parent_post);
update_comment_meta($comment_id, 'dsq_post_id', $comment->id);
wp_notify_postauthor($comment_id);
