You're right - this is a bug/oversight that will be fixed in the next maintenance version.
In the meantime you can fix it by adding the following code in qa-app-users.php:
qa_db_user_logged_in($users[0]['userid'], @$_SERVER['REMOTE_ADDR']);
... after ...
qa_set_logged_in_user($users[0]['userid'], $users[0]['handle'], false, $source);
You'll also need to add { ... } brackets so that the if ($countusers) conditional covers both statements.