First off, let me just say YARPP is an awesome plugin. Haven't had any problem with it until now.
I'm using a custom template for YARPP. I remember it being fine a day ago but it is now printing two of the same related articles. The custom template I'm using is the first sample you shared in your post here: http://mitcho.com/blog/projects/yarpp-3-templates/.
I've tried turning off "automatically display related posts" but no luck. The related article list is being displayed in custom category pages and as I understand it (which is not much), I have to manually use this code to call YARPP: <?php related_posts(); ?>.
Thanks for the help!