^ In the novel he was genuinely frightened of Bruce when he heard the Batman voice. It was like they were two different people he comments.
Ok I just reread the part where Lucius and Batman met.
The Dark Knight:
What Wayne had done with the technology Lucius' had given him was, in Lucius' opinion, pure evil. He had no doubt that Bruce Wayne was a good man, but he was starting to doubt Bruce's nocturnal alter ego, and the lengths that it seemed willing to go to. The lines that had been crossed... Maybe this was one of those three faces-of-Eve deals, different personalities inhabiting the same body. And maybe Lucius wasn't serving the good personality anymore.