Is there another way I can know for sure the controller box is CB3.1? Can I read the .urcontrol.conf file? If I can, what should I look for? The masterboard_version, the controller_box_type, both?
No, this is not updateable through a regular PolyScope/Controller update (.urup).
It is dependent of the motherboard in the CB - respectively CB3.0 or CB3.1.