I'm using your plugin with the foloowing modules:
Login with Facebook
Publisher (send posts to Facebook)
Allow FB Login to Comment (for non-registered users)
Integrate FB Comments (needs automatic publishing enabled)
The "Automatically Publish to Facebook Profile" Setting is set. My Facebook App is not in Sandbox-Modus any more and I changed my comments.php file in the theme like you described. My theme also has a wp_head and a wp_footer function call.
I don't know what else I should try. Have you any idea?