Plugin don't check when the user is registered, so you should use (f.e. comments.php)
if (( function_exists('math_comment_spam_protection') )AND( !isset($user_ID) )) {
instead of
if ( function_exists('math_comment_spam_protection') ) {
Related to "Add code to the comments.php of your theme. In the following an example for the Wordpress standard theme (Kubrick)" seeing on Plugin-Homepage of the Author
http://wordpress.org/extend/plugins/math-comment-spam-protection/