They may have been destroyed by wandering monsters. It's not out of the realm of possibility. They're supposed to start with at least one super strong guardian unit though....
I guess so, but the 1st turn hadn't started yet and I get multiple messages that the factions are gone.
I started over again. Now, during character creation, all of the equipment avaliable to the custom wizard is grey'd out. Also, when I try to cycle through various faces on my sovereign, all of the new type of face boxes stay highlighted (the face looks rather plan, but I currently have 6 different types of faces selected, including ones from different races and different sexes.)
Going to try quitting out the program and restarting a new game, perhaps something is borked the program out.
Edit: The full game restart seems to of fixed the problem. I still have the save of Janusk's army with the pop up messages of the minor factions being toast, if it would help.