If you look at inc/functions.php, and look for "function get_current_location()", you'll see that MyBB takes the current location (used in who's online) from a variety of variables.
You should go to your admin panel and look at the phpinfo page. Have a look at some of the variables like $_SERVER['REQUEST_URI'], $_ENV['REQUEST_URI'] and see if there is anything out of the ordinary, case-insensitive or pointing to the wrong location etc.
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