I think Jubal Early underwent the same type of brain manipulation that River did. He could have been the first generation of it, so he was extra-screwed up as a result of trial and error. There are a couple of things that make me think this, but what really hit me, is the scene when they're standing on the catwalk above the cargo bay and Simon is slowly inching his way towards Jubal, and Jubal whips out the gun without turning around and says "It's not your time." The way they filmed Early there, with him holding the gun straight and steady at Simon's head, never having looked around, it just seemed so simliar to the way River looked in 'War Stories' after she'd shot the three guys. I think even the camera angle was similar, but I have to re-watch WS to compare.
The other hints about why Early is the way he is are the conversation when River is in Early's ship and she says how his mom was glad when he went away. Also, when Early is talking to Simon when they first meet, Simon asks, "Are you Alliance?" which Jubal mishears ("Am I lion?"), and then Simon says (heh) "You're a bounty hunter," which Early also mishears ("No, you've got it all wrong. I'm a bounty hunter."). Jubal doesn't mishear anything else after that, and no one else questions him about who he is after that, either. Could it be some sort of brain implant thing that's making him slip on these questions? Is he just so trained that he sticks to his bounty hunter story (which I assume he actually is, but who pays him might be specifically the Blue Hand guys), and yet he's so messed up that he sort of hears things? I don't know. It just struck me as odd.
On a non-Early note, when Kaylee is lying tied up in the engine room, River calls her name and the sound of her voice is very dreamy, and extremely clear. After Kaylee says "River?" then the sound of her voice comes over staticky again, like she's talking over the radio comm. I'm not sure how to take that, but my hypothesis is that she's actually somehow directly talking to Kaylee's mind when she first says her name, and then is on comms afterward. But I have nothing to back that up. Heh.