Here is the setup:

Custom sovereign, with Hunter for History, Naturalist and Tracker for Talent, stubborn and inefficient for Weakness. 15 for all stats and 3 books: restortion, air and earth

Taking Altar with Fertile, Ressourceful, Hearty and Master scout

I start the game, found a city (giving 4 gold, 4 prestige, 4 research and 4 spell point), set 2 hut to be build and research warfare, take Equipment. Choose Civilisation, take farming (and set farm in the building queue) and continue the civilisation path. When the city levels up to level 2, my city produces 6 gold, 6 prestige, 6 research and 6 spell points. I save the game and exits it. When I reload the game, my city produces now 6 gold, 8 prestige, 8 research and 6 spell points. And if I save and reload it, the research and prestige will go the same way (+2 each)

Could someone see if they experience the same problem with this setup?