There wasn't a check stub that said $118,000.00, so that's out.
Have no idea what the details of the basement room might be, but I bet I can guess. See if it has something to do with cigars. If that's not it, I could probably guess a few more.
Maybe that is the thing - there was a check stub and LE knows this but never verified there was a stub as it may have been under some papers on his desk and the perp was digging through paper work and reburied back in the pile of papers.
According to the source, Karr wrote about a check stub on John Ramsey's desk in the amount of $118,000, specifics about a staircase in the Ramsey’s home and details about the basement where JonBenet was killed.
http://www.cbsnews.com/stories/2006/08/18/national/main1909118.shtml
(this one is dated from the 18th)