I was re-watching 6.01, and while I personally don't think that Bertram is necessarily RJ, there is definitely something up with him. In the scene where he's telling Lisbon and Jane to take a case far away from Sac PD, he says he is "many things to many people", and is just generally creepy through the whole scene.
Also, when Lisbon is in the house where Partridge died, there is a weird drawing on the wall: http://i.imgur.com/kHrVRS5.jpg.
Thoughts?