I think users awaiting confirmation arent shown on Who's online. Check if the usergroup id is listed in forum.php. Usually the usergroup id of Users Awaiting Email Confirmation is 3 it may be different on your forum. If it is then add that number to the skipgroups array in forum.php like 3,4,5 etc.
PHP Code:
$skipgroups = array(3,4);
Also set your usergroup permissions so that Users Awaiting Email Confirmation cant post on the forums.