The square headlights means you have a "F" series machine. The module on the side is called a BICS (Bobcat Interlock Control system)controller. The controller sends voltage out to the bics coil on your control valve to allow your lift and tilt functions to work and to the brake solenoid to work. As far as the controller saying it was updated or bypassed The Bics system has gone threw 3 generation/versions. The newest version 3rd generation has the green button to push to make the lift,tilt and brake functions to work. A yellow button is the 2nd. generation. The seat light flashing on the controller could mean a couple of things depending on how many flashes and how quick but usually suggest that there is an open or a short in that circuit. That can be also true with the aux. light flashing. The aux. working on their own could be caused by a couple of things. There are coils and stems on the top of the control valve that are energized when you use your electric handles. Sometimes those stem will stick open do to rust or debris causing the symptom you are talking about with the grapple. The stems and coil can be swapped with each other so when the problem come back you can swap them to see if the grapple will close down as soon as the machine starts then you will know you have a bad stem.Without actually being there I hope this helps.
