Quote: Well, there was one other time I discovered: I pointed at my wife who was looking out a storm door. The reflective surface confused the autofocus.
You must have a very shiny wife.
Quote: The only mystery left? Why didn’t anyone suggest this to me?
Because we all assumed you'd read the manual
The autofocus can still get confused, even when on spotfocus. In the trees with chimney scenario if there is a blustery wind the branches will at times whip across the focussing spot enough that the camera will re-adjust. Very annoying.
To counter this there is a custom setting to allow the OK button in the centre of the four way switch on the back to hold focus for as long as you keep holding it down. This saves you switching to manual mode as sometimes these situations are transitory and you may wish to be in Auto all the time.
Other situations are in crowded localities when people walk between you and the focus subject or when filming across a road and vehicles are moving across the shooting path.