To reproduce:
- Add a mod with mod settings (I tried it with Auto Manual Mode and Rotate vehicles)
- Load or continue a game
- Go to the (esc) menu, then Settings, and Mod settings
- Change a setting (I changed a boolean Player setting)
- Confirm
- Go back to Mod settings (without closing the menu)
- Setting now looks like it's back to its original value (I expect this to show the changed value, because I clicked Confirm)
- Exit out of the menu completely, back to the game
- Then go back to the Mod settings (step 3)
- And now the setting shows the change from step 4