First of all, do you have any proof that all (or even a significant majority) of police forces label items like flashlights? I can certainly see them doing so for things like guns/tasers, but a harmless and relatively low cost item like a flashlight would seem like unnecessary overkill for many police forces.
Secondly, this illustrates a major problem with the whole "insider theory"... the Ramseys are smart enough to realize "The flashlight may have evidence... we have to sterilize it", but somehow aren't smart enough to realize that it would also look suspicious to not dispose of the writing pad. Or if they are getting rid of evidence like the roll of tape, why not get rid of the flashlight while they're at it?
Still a problem, because the flashlight (if it indeed belonged to the Ramseys) would be in a different room that the train materials. You'd have to come up with a plausible scenario to explain how Burke would have had easy access to both. (Not to mention a scenario that would get her to the basement in the first place.)
Granted, Dr. Phil isn't exactly a paragon of moral virtue, but given some of the information presented by CBS (As described here) appears to be absolute bunk, I wouldn't exactly say CBS has the high ground either.
The 'stun gun' theory was originally put forward by Lou Smit, a retired police detective who was asked to investigate the case by the District Attourney. Smitt had a very solid reputation, having worked on many high profile cases. He should have adequate knowledge to identify the marks that would be left by a stun gun.
And stun guns can leave marks on the skin, perhaps not in all cases, but it does happen.
http://www.ncbi.nlm.nih.gov/pubmed/12762539
Or:
http://www.cbsnews.com/news/searching-the-stun-gun-theory/
Dr. Michael Dobersen, a stun gun expert and coroner for neighboring Arapahoe County, also believes the marks on JonBenet were left by a stun gun. To prove it, he used one on the skin of an anesthetized pig. "The marks are similar in size, shape and color and are a certain distance apart," he says.
Once again... evidence shows that JonBenet was still alive when the garrot was used. If Burke did hit JonBenet and contributed to her death, not only would the parents have to act to cover up the murder,
they would have to strangle their still living daughter as part of the cover up, rather than actually getting her medical attention.