for the first point, can you take 3 screen shots, 1 of them before they leave the settlement, one when they've moved out and one after they regain the traits. You only need to do it for one of the characters that is showing this behaviour.
[edit]Wait - don't forget as per Tone and DVK in
this thread, there is a 2nd rebellion that is going to happen. You will get some governors/generals who rebel no matter what you do, hell you could set them up with a personal harem and it would make no difference. If that is where you are at, then you need to accept it is going to happen and try to recover your Empire.
However, the rebellion seriously should not be delayed until 120 settlements the first rebellion is in the first 3-5 moves when the Roman rebellion occurs in Southern Italy, in the 2nd which is much more extensive, it should be about 85 settlements.
It usually fails if a save has been corrupted somewhere along the line.