I had a similar thing in my current written up game. I don't have the MCP installed at all, but upgraded to REV 1069
The Mayan's, capital , Mutal stayed at size 1, I just assumed it starved there. Montezuma, who was spun off as a rebel, with a size 3 capital, starved his 2 cities down to size 1, but others grew???
Other civs all seem to be growing, maybe just a coincidental occurrence.
*Edit
I had a look at the game;
1. Greece is size 1
2. Iroquois are size 1
3.Khmer are size 1
4.French are size 1.
I've come out of a dark age from volcano, over 200 yr's ago, so not that??
NO MCP, STANDARD MOD. REV 1069