Is it possible to have too many cities?
Many people have the same issue. It seems for most of them to have something to do with the darn number 64. While some people on the forums of 2K Games just think that there's a bug in the code relating to the "special" number, others think it's all about the fact that this game is a 32-bit game, which means it runs out of memory after a certain amount of cities captured/loaded or something like that.
While reading through the posts, though, I just noticed that this is from 2010! That's kinda sad, because now I can't tell you if this is still an "official" bug or already fixed in some way. I can't find any other forums or posts where this problem is being discussed.
You can find all the information here.