It has to do with persistent settings (options, player number, advanced settings, etc) carried over from previous games or other mods. This info is saved at the end of config.ini (the "[UserSettings]" section) and in files in the cache and ModUserData folders. I'm trying to make the mod fully resistant to this sort of thing in v13. So with v13 you will no longer have to mess around with config.ini and deleting folders to avoid savegame corruption. The good news is that this effort has allowed me to re-enable Advanced Settings for the mod. Even better, all of the settings are persisted specifically for the mod. So if you always play Éa at King difficulty on PerfectWorld3 map with 10 City States and all Sidhe opponents, then those settings will be there the next time you load the mod (and it won't affect settings for non-modded games or other mods).