Had this same problem, even sent a save game file to someone (think it was Daynarr or God Emp) who tried the save. For me it was freezing up on the turn of the Sergetti, (turn 6) and I had to go in manually and finish the turn, eventually had to surrender this empire plus the Xi'Chung as they both froze up. It was Modpack 1.5(I think) and the races were manually loaded to thier expert level in racial points. Have not really tried the current modpack. Just using straight 1.3 patch plus the addition of the Narn, EA, Toron, and Darlok races. So far no freezes. Sorry I can't be of much help other than to say I too have had a few problems but put it off to my fritzy computer.
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"The Empress took your name away," said Chance.
Owen smiled coldly. "It wasn't hers to take. I'm a Deathstalker until I die. And we never forget a slight or an enemy." -Owen Deathstalker.