Not accusing anyone, just a side theory.

Before Patrick's family was murdered he was helping the "police" with the RJ investigation.  We never know who the "police" are but you are lead to believe it is the Sacramento PD (You are lead to this because in season 5 episode 5, "Red Dawn" when it's a flashback and Patrick first goes to the CBI to look at the RJ files Lisbon says the files were transfered to them a few months ago from Sacramento PD).  
2 points:

1) I think it's very strange that no one ever mentioned Patricks work with the SACPD (or other police) prior to his work in the CBI.  Wouldn't Lisbon be able to figure that out?  They seem to ignore that part of his past.

2) I bet RJ was the one that got Patrick a job at the CBI.  RJ made sure the files were transfered there (knowing Patrick would eventually come in) and made sure he got a job there.  Minelli's and RJ's first meeting did seem awkward/tense and Minelli was extremely open to the idea of Patrick accessing the RJ files.  This points to Virgil Minelli being RJ or working for him but I defintely don't think he is RJ.