I got some crashes on Hayasdan turn when testing the rebelling cities fix on the internal pre-0.81a (part of the reason why it took so long before releasing it...). We think it's another bug that has been masked because the symptom is so similar to the rebelling city CTD. It had the same characteristics of yours, one crash first, then another a few years later that is repeatable. Unfortunately it was an all-AI game, so we couldn't look around to see what was wrong.

I'll take a look at your savegame. I hope it's the same thing, so we can finally start hunting down this sneaky bug.