I came across this issue when I copied the shortcode (listed on the settings page) into my php:
<?php echo do_shortcode('[fbcomments][fbcomments url="http://3doordigital.com/wordpress/plugins/facebook-comments/" width="375" count="off" num="3" countmsg="wonderful comments!"]'); ?>
To resolve this, just remove the 2nd fbcomments, so it should look like this: <?php echo do_shortcode('[fbcomments]'); ?>
You may need to turn off the display options to disable the auto hooking into the post/page.
Hope this helps.