I don't know if this is related, but I'm playing two different franchises. I tried to have different settings in each. But if I set Scouting to manual in one, it sets it to manual in the other as well. Those settings seem to apply to all franchises, which I don't think it did before. I would set everything how you want it, and then go into Data Utility and manually save the franchise. Then exit and reload the franchise to see if the settings were retained. If they are not, or if they are changing after that without you changing the setting in a different saved franchise, then I would think it's a bug.