1. Check the diplomacy screen. Are the portraits of the AI players shattered? If not, they are still alive somehow, they either have a planet you missed or they're Vasari Loyalists and they have a titan, capitalship or starbase still alive.
2. Are you sure you turned allied victory on? If not... *duh duh duh*... you must stab your friend in the back, for only one player can rule the universe this day 
