Ok, kept playing and reached 10-15 cities on my medium map game.
Prestige broke - All my cities have growth of 0.1 regardless of actual prestige in each city.
The city penalty is listed as very low 0.3, 0.4 and is properly reduced if I raze a city. However all cities remain at 0.1.
Enchanting a city 4 times for +1 prestige per enchant does nothing. The detail window will report a final prestige value after all modifiers like 4.7 but on the cloth map it will still say 0.1
Is this a case of hidden modifiers? Most of my cities are lvls 1-2-3 and I'm about 600 pop. nothing big.