The torch was not part of the original crime scene at 5:52am. Someone placed it there intentionally, wiped of all prints sometime in the later morning hours.
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Why should the timing matter? Who thinks Burke wiped the flashlight clean and dumped it in the kithchen?
Apparently Patsy never moved far from her location once the first officer and friends arrived, she was under their eyeballs, only JR had freedom of movement.
JR has slightly more knowledge of the crime-scene than he should actually have for someone who took a sleeping aid, slept well, and awoke to find his daughter kidnapped.
My money is on JR tweaking the crime-scene all morning at every opportunity, probably even relocating JonBenet from the crawl space to the wine-cellar, then leaving the flashlight in the kitchen.
If he had been caught with it, he could always say: I was using to look for JonBenet.