Does your apocalypse folder contain 12 items and have you never touched it before this?
My theory is that the entire scenario folder must be exactly the same. Same size, same names, same number of files. So even if you have an extra irrelevant file, like a saved game, it will assume that the scenarios are different and use the default civ files.
[This message has been edited by kobayashi (edited March 10, 2001).]