BBM...Remember the "clever little clues"" comment? JR also repeatedly kept himself distanced from admission of the flashlight being his with certainty. And, doesn't it make sense that with locked doors on the main floor, an intruder would have had to use that broken window as an access point? For a while the window with the hole in it looked plausible, even to Lou Smit. I have no doubt that in any conversation the R's had with him, there would have been every attempt made to cleverly suggest the broken window should get greater investigation. Once Lou Smit made the pronouncement of possibility of an intruder, the seed was not only planted but watered and fertilized. Let's remember too, that one of the first suspects offered up was LHP, and she would have satisfied the "it's an inside job" comment as well as being someone who would have known how to use the broken window to make an entry (or have someone else use the window...like her husband). Pretty handy to have a personal employee to blame who needed money, who was known to think of JB as a bit bratty, who wondered if the R's might not be worried about something happening to her because she was allowed to be outside in the neighborhood playing alone at the age of 6, who would have known about the basement layout, and who also was actually able to identify the flashlight as belonging to the R's.
Yes, it makes sense that the window would have to be used if the doors were locked. It also makes sense that someone with a key could have entered and locked up when they left.
JR claims all the doors were locked, eliminating the possibility of someone coming through an unlocked door. That only leaves someone with a key, or someone coming through the basement window.
But, since the grate is in place and the web intact, the idea that someone came through the window makes no sense.
If there was an intruder, he/she used a key to enter and the window really was broken months earlier. If it's RDI (and it is) then JR made up the story about breaking the window himself to cover the fact that the window couldn't have been the entry point. That still leaves someone with a key as a possibility.