That's a good question. I don't know. But clearly the Ramseys were able to mount a really good defense and I think that is what frustrated the Boulder police so much.
There could also have been internal contradictions in the case. Things that pointed to the Ramseys, things that pointed away from the Ramseys, things that pointed to a family member or friend, things that pointed to an intruder, and things that pointed to a poor investigation.