I think we are stable enough now that the rushing pop-ups are starting to cause an issue.
I hit "next turn" and the computer alerted me to a bear attacking my scouting peasant. Because there were only two models it initiated auto-resolve automatically, but at the same time, I needed to select a new spell and one of my cities had empty queues.
I could maneuver around the world, select units, and issue orders, but for a good two minutes, I was unable to open any windows (city, training, building, Esc Menu), or hit "end turn".
I though it was going to crash pretty good, but after about two minutes everything popped up all in succession, one after another as I closed them.
As nice as the multi-threading is, I think that the computer getting impatient with the pop up windows (opening a new one before you can resolve the previous one) is likely to have been causing a lot of the instability issues in previous patches.