— I don't think what you are saying is correct, or maybe I didn't quite understand your message.
"Compare instance variable" event picks instances. If I use "Compare instance variable id=1", this will pick all instances with id=1.
So naturally I assumed if I use choose(0,1) in this event, it will first choose a random number (0 or 1) and then pick instances with id equal to that number.
But what happens is that this event actually checks each instance separately, and for each instance calculates a new random number and compares id with this number. So it can pick one instance (which seems correct), but it can also pick two instances or none.
See this example:
dropbox.com/s/tsje45mszx2vepp/PickWithChoose3.capx
Also, resetting opacity on start of the layout doesn't fix the issue, because all objects are reset anyway when the layout is restarted.