In one episode when 2 cops died  and Jane  said RJ is getting sloppy and i remember the way Virgil Minelli addressed the media , looked very personal. One could argue how do you expect him to react when two  fellow cops being murdered. True but if i was in his position as the head of the unit i would have stayed and helped find the killer but no he nicely  resigned. He knew he was getting sloppy so he had to leave in order to stay focussed. He also asked Jane to join CBI and asked Lisbon to give all the RJ files, so that he could monitor him at the same time  it could present a greater challege. And also in another episode in Season 5 he got a call from a FBI director Agent Shultz or someone and asked him to give updates on RJ findings by Jane and in return he would get a top ranked friend from FBI. May be thats how RJ knows all FBI movements. And also there was no need of that episode to show how jane started working for CBI. May be earlier but not in Season 5 unless they wanted to remind us of Virgil Minelli because at the end they just cant all of a  sudden say he is RJ as he didnt had any part to play after that cop killing episode in second season.