There was a bug in the config saving routine that is now fixed, but some of your configs might already have saved broken faction colors - e.g. blue for resistance, gray for metropolis.
If you experience this, you can simply go to Settings -> Open user folder in explorer.
Then edit the config.json file (it will be highlighted) and remove the entire "faction_view" section.
Alternatively for a quick solution just press Settings -> Reset all settings to factory defaults and configure your game again from scratch.
Sorry for the inconvenience!