As Chris mentioned earlier, Rondo's lower body mechanics are a lot better on his jumper. His release seems cleaner, and his follow through more pronounced.
I have no idea why he isn't better at the FT line. Probably mental. Rondo's best shooting comes when he's not thinking and just reacting, like at the end of the shot clock. He's a quick twitch guy, and FT shooting is a slow twitch activity. I'd suggest working with a sports shrink to teach him how to clear his mind when at the FT line.