So, a strange thing happened. The Terran Alliance disappeared, and has been replaced with a generic Create-a-Race. I've tried uninstalling and reinstalling, and it's still gone. I don't use any mods, and I can't restore it properly (as in, rebuild it), it always comes off as some permanently evil faction that lacks the built in bonuses.
Any suggestions would be appreciated. I like to use the Terran Alliance as a base for my personal faction (which has also disappeared).
