Here's the story:

- I was playing with Unrestricted Leaders turned on.
- Willem van Oranje was my leader and Portugal was my civilization.
- I was playing on a Terra map, Epic speed, Standard size, Noble difficulty.
- No advance start.

I reach the new world with my Carracks, get some barb cities, and settle one of my own. I then build the Palace in one of the former Barb cities. Once that is my capital, I liberate the cities that are in the old world.

So I make a colony of the old place instead of the new place. And that colony ends up being Portugal, led by Joao II.

That's weird to me and I'm pretty sure it shouldn't be happening. Two of the same civ in one game? Unheard of.

I have a screenshot of Joao II talking to me and displaying how we are both Portugal, yet are both separate.

I also have 2 game saves, one on the turn that I liberated them (but the save is before I did so), and one a couple of turns after their liberation.

I'm pretty sure that it's a bug for it to happen and I'm pretty sure the game just got confused because I liberated the old world and I'm sure it also has something to do with the Unrestricted Leaders, as the game may have gotten confused with me playing as Willem. So I'm hoping that this will help.

Actually it is not a bug - but an intentional game mechanic, though it causes so much confusion that it will probably be changed. At the moment the game does indeed try to max out the civ that creates a colony (i.e. it will assign american leaders as long as there are any if america spins of a colony etc.). With unrestricted leaders it probably will never run out since it can assign any leader as civX...

but in the new patch the are fixing it