I do not know whether I am right or not, but, Patrick Jane is very clever guy and I think he already has found who RJ is. He is just proving with clues for himself in order to be sure. In ep 2, season 6, Bertram came to the team and gave new order about car explosion and, then he talked with Jane about Lisbon and RJ. After asking from Jane informing him about RJ case and clues, Bertram walked away and Jane looked at Bertram's steps and sound of his walking... And Jane's face a little bit changed when he was looking at it, because Jane met with RJ when RJ saved his life and if you remember, when RJ has walked away from Jane, there was sound of RJ's walking as the same is ep2s6. 
Any comments?