I digged deeper and deeper. For the sake of completenes querystring parameters is set to true.
The message of Unable to locate the specified class: Session.phpUnable to locate the specified class: Session.php is coming from system/core/common.php line 187.
The session class is a bit different from the others:
<root>\system\libraries\Session\Session.php
So it is one level deeper then the other libraries.
In my autoload.php I have the following:
$autoload['libraries'] = array('database', 'user_agent', 'session');
In my controllers I don't have load session calls any more.
I hope some one has a clever moment and wants to share this!
John