You appear to be missing some code from your header. You need to copy & paste the following code into your header file:
<link rel="alternate" type="application/rss+xml" title="<?php bloginfo('name'); ?> RSS Comments Feed" href="<?php bloginfo('comments_rss2_url'); ?>" />
I’ve had the same problem with WP Stats. There doesn’t seem to be a way to fix it. As to it messing up your popular posts, what plugin do you use? I use a modified version of popularity contest and have never had a problem with it.
