1. Start a new game with any mod that creates map settings or per-player settings. (I've tested individually with Cerys, Variant Hotkeys, Auto-Switch Techs, Maraxsis - all of them have this bug.)
2. In game, open the mod settings menu.
3. Change the value of any map or per-player setting.
4. Press "confirm".
5. Immediately after pressing "confirm", open the mod settings menu again. (Before resuming the game.)
6. Changes made to mod settings have been reverted to values before you changed them.
"What did you expect to happen instead?" I expected that in step 6, it would still have the changes I just confirmed.
"Does it happen always, once, or sometimes?" Always.