All the factions? Including the Mongols, Timurids, Aztecs and REBELS?
That might be the problem right there. Aztecs are normally frozen until you encounter them, while the other two are dead until resurrected. Making them playable messes up their settings big time. Rebels should not be messed with at all.
Since you can't change the settings in an ongoing campaign, why not just take it that the plague killed off all the natives and take it from there?
Turks in America... have to try that one day.
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