Happened to me too on my immortal game... Byzantium, of all civs, got completely wiped, from a 10 city empire. and most others lost 3-4 cities permanently. In my mind, the problem resides not all that much in the fact that cities turn free when you hit dark ages. It's also that walls are very strong (too strong ?) and hard to defeat, and that free cities get the best possible units at the moment of turning. And then start pumping out others (unless they stupidly produce builders ;-) ) All this is compounded with the loyalty pressure from free cities, which is new. It just snowballs. It has gotten to the point where I have decided to simply declare and attack my neighbor Maya before she falls to this snowball, instead of allowing her cities to turn free and becomes twice as hard to attack or defend against. Doesn't make sense. Maybe, in the end, the QA and Dev teams should reassess the free cities loyalty pressure.