I think that is why this case has not been solved. Because it is assumed it was the parents. It does look like it is, until you consider that the window was open, the debris at the window WAS disturbed, (except for ONE cobweb) and there was a suitcase up against the wall with a shoe print that did not belong to anyone in the house. not only those things but there was a black scuff mark on the wall where someone pulled themselves up into the window using the wall as kind of a brace to do it. I think the parents didn't really know what to do. If it was my child, I would have immediately, without thinking, picked her up and rocked her. So who did the shoe print belong to? It was never known, and it wasn't a size of anyone in the house, and a similar incident happened a few houses down. So for me... it was never the parents, but because the police were sooo incompetent, and unreasonable it got totally screwed up from the beginning. I actually always thought it was an older adolescent, probably a neighbor that lived in the area and maybe even an older friend of the kids. I can't remember if the same incident in the neighborhood was before or after JonBenet. If it was before, the neighbor girl might have been the first attempt at a victim. I always thought it was an older kid though, (not Burke BTW).
Then he felt remorse, and he knew her, so he covered her body.
"I think that is why this case has not been solved. Because it is assumed it was the parents."
Plenty of investigators such as Lou Smit, all the Ramsey's PIs, and DA Mary Lacy in conjunction with LS and his "Apple Dumpling Gang" refused to believe the Ramseys were involved and the best lead they could come up with after twenty years was that delusional faker John Mark Karr.
"It does look like it is, until you consider that the window was open, the debris at the window WAS disturbed, (except for ONE cobweb)"
Have you looked at the crime scene video of that window and cobweb? See here:
http://www.thedailybeast.com/articles/2012/07/18/new-clues-in-jonbenet-ramsey-murder.html
Not only do I see little disturbance in the twigs and foliage lining the bottom of the window well but it's fairly obvious simply judging by Lou Smit's demonstration of how he climbed through the window that no one could get in without disturbing that cobweb. It's not a big window, it doesn't even open all the way, and his entire body fills the frame as he climbs through. Had there been a cobweb included in his demonstration it would have been wiped out. Laura Richards, a slender and athletic woman, demonstrated this on the recent CBS special. Not only was the cobweb mostly wiped away when she entered, but it was completely gone as she tried to climb back through, as it was where she would have to put her hands for leverage. She also described the climb back up as not impossible but very strenuous.
"and there was a suitcase up against the wall with a shoe print that did not belong to anyone in the house. "
I'm not sure if you are conflating the HiTec boot print in the wine cellar with the supposed footprint on the suitcase or not. I can't find the picture LS used to demonstrate the "footprint" but it was far from clear. It likely wasn't even a footprint, but even if it was there was absolutely no way to say it didn't belong to anyone in the house because it has no identifying features. LS is the only investigator who looked at the picture and saw any kind of print there.
"not only those things but there was a black scuff mark on the wall where someone pulled themselves up into the window using the wall as kind of a brace to do it."
John Ramsey claimed that he climbed in through that window himself the summer of 96 wearing only his shoes and underwear, so wouldn't common sense dictate that he is more likely to have left the scuff mark than a stranger?
"So who did the shoe print belong to? It was never known, and it wasn't a size of anyone in the house,"
You must be talking about the HiTec print here. Fleet White, Fleet's son, and Burke Ramsey have admitted he had a pair of HiTec boots. Burke spent plenty of time in the basement playing with his train set and admitted to going into the wine cellar at some point to sneak peeks at presents that were being hid there. Verdict: It is far more likely that Burke left the print at some point before the murder and it is irrelevant to the case. As to your assertion that it wasn't the size of anyone in the house, that is incorrect. It was not a full footprint, only the "poon" or the logo on the bottom of the boot saying HiTec. From Perfect Murder, Perfect Town:
"The imprint was of the "poon"-the area on the sole at the heel where the brand name is stamped. The size of shoe couldn't be determined from the imprint, since the poon is the same size in all shoes, the better to advertise brands."
"and a similar incident happened a few houses down."
I know what incident you are referring to but here's my question: was that girl six-years-old (no, I believe she was 14-ish), murdered and posed and hidden in her basement (no)? Did the perp leave behind a rambling fake ransom note (no)? The only (seeming) similarity is that some creep broke into someone's house and violated a young woman. If you discount the idea that any intruder was involved in JonBenet's death, there is no commonality there whatsoever besides the fact that they went to the same dance studio. And to answer your question, this incident did happen after JB was murdered. Meaning either the perp completely switched tactics and targets (penetrating a kindergartner digitally or with a foreign object vs raping an adolescent) and basically devolved from following a highly complex and convoluted MO (faking a kidnapping, hiding the body, wandering all over the house to get supplies) to a fairly simple one (going into a girl's bedroom and raping her but leaving her alive) - or they are two different perps altogether.
As far as the DNA goes, it has been known almost from the beginning that the fingernail DNA is meaningless. There were two different samples found which were too weak (2-3 markers I believe, belonging to a male and a female) to conclusively link to anyone. But more importantly, the coroner admitted he clipped her nails with clippers that were not sterile. The most likely explanation is that those DNA traces are contamination caused by clipping the fingernails of previous autopsies, not two killers. The underwear DNA has recently been debunked as unreliable as well. Charlie Brennan of the Boulder Daily Camera and News9 got the DNA reports and had independent analysts look at the result. Their conclusion (and the conclusion reached by the original Bode lab techs in the test results, as it was revealed) is that the underwear DNA is a composite of three people, JB and at least two men. The conclusion was that it is basically an amalgamation of DNA belonging to no one. It does not rule out the possibility of an intruder, but it does not rule out the Ramseys either. It is useless. We're talking about the most notoriously contaminated crime scene in history and evidence taken before anyone could even conceive of touch DNA, much less prevent it contaminating the evidence. As Kolar points out in his book, the various deposits of trace DNA on her clothing and ligature would ultimately point to six different different people being involved. So you're left with these questions: did six people break into that house that night through the cobwebbed window? If so, why is it that the only trace of them comes from minute samples of touch DNA found on her clothing? And if only one of these samples belongs to the perp, how are we to figure out which is the important DNA and which is the meaningless DNA?