The Jotnar are in my game too. I have made it to around Turn 300 and now I am getting CTDs constantly. I save after each turn and usually if I go back 3-5 turns and 'play differently' I find I am able to play on.
However, in my current game, no dice. I have tried going back, deleting units, whatever, but did not delete the Jotnar.
Are you saying that the AI Jotnar could be causing mid-game CTDs and to try deleting them to save my game?
I thought I had selected the option to not choose the Jotnar or Scions randomly for the AI, but I forgot.
Thank you.