I can't say I've ever encountered this bug myself. It sounds vaguely similar to the situation I had when I first tried to play Civ - if I encountered any city, the game crashed (I suspect this was due to old drivers, but am not sure). Is it possible that PTW was patched sometime after this game was started, and thus the current version is not the same as the original?
It also is odd that the barbarians would have a city. Are you sure it isn't simply a barbarian camp for Mayan barbarians? If the barbarians actually do have a city, it is indeed a bug I'm not aware of. Perhaps someone at one of the Civ sites where you've seen it mentioned in the not-recent past will be able to tell you more about it.