I think the clue in 06x01 Bruno Heller was talking about (if there's one) is right in this scene. Not a theory, just some thoughts.

http://www.youtube.com/watch?v=5cXoK094QS8

- Thers's a red thing on the table (00:10) but I think this is irrelevant

- Look at PJ's face at the moment when Partridge comes (00:30), could it be that some element made him realize Brett is RJ?

- 'You truly don't know?' Ok now imagine PJ and RJ are two masterminds and RJ is Partridge, it could be that when they're facing each other (01:35), both of them know PJ has figured out that Partridge id RJ, that is why in the same episode, Partridge fakes his own death to try and make PJ believe he is not RJ.

- There's the same cop walking around in the background. Look carefully (00:14 by the boat, 00:27, 00:48, 01:13, 01:33). Why would he walk randomly around the crime scene?

Just thoughts guys, peace. <3