You wouldn't by any chance be trying to repair any other factions government building? I captured a Thracian city and planned to give it to my allies, the Macedonians, and with that in mind I decided to repair the lvl 4 Mac gov which I found in the city. Well, I got a CTD immediately after clicking the end turn button, and I'm pretty sure that this was the reason. Atleast it didn't crash once I had removed the building from the queue.
Nonetheless, I'm also suffering from regular CTD's as the Romans, after battles. But their not (atleast so far) reproducable...