Ok, I found the problem with my game.
When the things postet in
http://forums.civfanatics.com/showpost.php?p=8777240&postcount=559 happen, the game continues normally for a few turns, but any save after this point will load with the error:
Traceback (most recent call last):
File "CvWBInterface", line 18, in writeDesc
File "CvWBDesc", line 1533, in write
File "CvWBDesc", line 466, in write
RuntimeError: unidentifiable C++ exception
ERR: Python function writeDesc failed, module CvWBInterface
and then crash 1 or 2 turns later.
I deleted the Barbarian City which is to turn to this Minor Civ and everything is fine again (have to test another 20 turns to be sure).
I'm at least 20 Civs away from the 50 Civ limit, but so far up to 10 Civs have emerged from Barbs. Perhaps there is a bug in this routine. Will wait for the next Civ to appear and see if this happens again.
I don't know if this is common when new civs emerge or a hint to a bug:
PY: Revolt - WARNING! City State have cities but no capital on turn 541
Playin' on