I've played 6 games now since the campaign, and have noticed a few more bugs.
First, my estimation for time to complete a research assignment is always wrong in the middle game, I finish research projects 1-3 turns slower than projected.
I think this must be research treaties. At the start of the game, research works correctly - I always finish a task in the appropriate time. At the end of the game it is always accurate as well, but by then usually no one is willing to let me extort a treaty from them (especially if I've broken treaties)
But in the middle of the game I usually have research treaties from 2-4 civilizations being sent my way. It seems to me one of two things is going on here, either:
1. The value of research treaties is being overestimated in the time to complete calculation, leading to estimated values that are smaller than actual values. (Saying something will take 7 turns when it really will take 8); OR
2. You do not actually receive the research points from the treaties from other civs. In this case, the estimator is wrong, but the bonus research points never actually get calculated.
All other variables were corrected for. I was never spied on on a research building to change my own production, I never changed my sliders (100% production, 50% on research slider), my economy could always afford all of my spending on everything.
Thanks