Interesting... But that still doesn't explain how the A.I. civilizations or I lost. Their entire populations vanished in a single turn and were replaced by those of my allies. Plus,when the Slyne fell, there was only one other civilization remaining that wasn't part of my alliance, and they held the most military power and nothing else.
I was playing my first single player game in GalCiv3, I had four A.I. allies and eleven A.I. enemies. by turn 285 I'd spent over 16 hours on the game, and I had first place in influence, population, research, construction, and number of colonies as well as fourth place in military power. I noticed something strange that would occasionally happen where a popup would say "Such and such civilization has been defeated" and then the next turn all of their colonies, ships, and starbases would belon