Hey,
currently I try to implement your mod to my modpack. My friends have made already big progress in gearing up so I decided to editing the default values.
I pretty enjoy the idea to have a global multiplier and make my friends scream when your ancient beast first appears near their homes :)
So I created a local copy with vanilla Minecraft only with JEI + your mod (1.9.15 with Forge 14.23.5.2860)
I always make a fresh instance. So that I can try to reproduce any issue/bugs where no others mod/config could conflict.

Reproduce:
Join a world and hit ESC to navigate to Mod Options ->AncientBeast -> config
Now change any value…

Here is my Example:
I tried to change false to true for Zealot Spawn Everywhere.
I also wanted a health boost for Vessel and set his value to 100.
Now hit done and restart the game.
After booting up again a look in the config confirms that nothing was touched…

I have no idea why it doesn't works, for now use ancientbeasts.cfg which should be in the config folder

Already did that with my editor of choice.
I just wanted to let you know that issue.

I can confirm it doesn't work with version 1.9.99999.jar either, might be best to disable it for now as it's been confusing why the config changes don't work

just edit the .cfg directly for now, I still haven't quite figured out why it is so broken.

Fixed it with latest alpha release