My GOTM = ruined?

[Little Sicily]

Well, this was the first game I've ever won by military so I got a little confused. I had eliminated everyone from the game save the Sioux, whose wall-mounted phalanxes had stood up to my crusader swarm tactics right into the 17th century. Then someone shot me in the face with a clue gun and I started building diplomats. Soon after, the walls came down, the defenders died, I saved my game, and marched in. The game didn't end right away. I finished my turn, still no game end, so I went exploring. The sneaky sioux had run off and founded some cities while I wasn't looking and thus I was forced to bring them down. Save, march in, repeat. Finally I got the message "Sioux Civilization destroyed" and thought that was it, but the game still didn't end. Did I miss a civ? So I saved and started exploring, but as soon as the turn ended, the fireworks started, I had won. The rules page says that my save game is now useless (I kept saving over the previous "final" saves), and I also clicked past the power graph, so I only managed to capture the final score. So, is my game ruined? Am I not allowed to submit it?
If so, I'll know better next time. I'm off to play the civ III GOTM now.