Hi thanks for answering.
After reading thru your post and troubleshooting I have found the issue. They have changed the ability for the ai to queue the command to take over and pilot the ship. A couple weeks ago, I would be sitting in the seat, ask the ai to take over, then the ai would wait for me to exit the controls and they would take over. Easy peesy.
Previously I didnt have the ability menu on my setup so after cramming that in, I can now order the ai to pilot the ship as long as I am not sitting in the seat!
So thank you for helping, that nudge about what happens if Im off the ship etc was just what the Tenno ordered :D