I didn't check the quest files which could cause the Tower of Judgement stuttering, because there is a workaround for that.
I can't find the thread now, but someone suggested that if you wait in front of the Tower of Judgement entrance until the walking souls reach the entrance and disappear, there will be no stuttering. It worked for me.
But since I had no workaround for the crystal room problem, I had to find the solution myself.
