Hmmm...that is odd. Isn't the base folder under SW:JKA > GameData > Base? Not SW:JKA > Base? Check for a gamedata directory. I could just be dumb, though. Plus, I think you have to assign GTK to the gamedata folder, so since you didn't, it creates all of it's files in a folder called base (usually merged with the one in gamedata), rather than the actual base.