I'm looking into this right now, it's still eluding me as this issue relates to the interface with NativeOptions and ConfigHelper.
It's a silent crash which is very annoying to pin down.

If you would like to try report it (MAKE SURE YOUR NAME ISN'T IN IT), for windows look in:
C:\Users\userName\AppData\LocalLow\Payload\TerraTech\output_log.txt

Additionally if you could list the mods you are using, that would help too

I have pushed some fixes which might have resolved the issue.
If it persists, please let me know

I have found and fixed yet another issue that may be related to this - apparently disabling "Enemy RTS A.I." results in a silent crash which caused settings to not save properly

can confirm that enabling "enemy RTS A.I." does allow saving of settings