I made it work with my custom post type by going into wpfp-page-template.php and replacing
query_posts(array('post__in' => $favorite_post_ids, 'posts_per_page'=> $post_per_page, 'orderby' => 'post__in', 'paged' => $page));
while ( have_posts() ) : the_post();
echo "<li><a href='".get_permalink()."' title='". get_the_title() ."'>" . get_the_title() . "</a> ";
wpfp_remove_favorite_link(get_the_ID());
echo "</li>";
endwhile;
with
foreach ($favorite_post_ids as $post_id) {
$p = get_post($post_id);
echo "<li>";
echo "<a href='".get_permalink($post_id)."' title='". $p->post_title ."'>" . $p->post_title . "</a> ";
wpfp_remove_favorite_link($post_id);
echo "</li>";
}
Hope that helps someone.