Try taking a look at the SMAC Academy at CGN. Buster has written an article that explains how to fix this problem, I believe.
This email from one of the 2 guys I'm doing an email game with:
"When I play my game, after taking Joe's last base I
get the interrigation screen then it gives me the GAME
OVER screens with final score and the like.
Then it offers me the SAVE GAME screen with my own
picture on it, when I press either thing, it goes to
the main menu."
Any idea of what's going wrong here? Why won't it let him save the game? If you ask me, it seems to think that it's Joe's turn at that point.
Briefly, you need to replay the turn where you take the last base of the player, and he has to use a unit to disband the base.
He then drops out of the game and can save it and send it on to the next player in the turn, and the game goes on minus the defeated player.
Thanks for the quick replies: it was exactly the right answer. Now, we're just waiting for him to send his next move.