He said "I'll never tell" in one episode, I forget which, but I had the impression that he was saying to himself he would never report anyone as a Cylon.
Hirogen Alpha said:
I don't remember, did Baltar sabatoge the machine to give everyone a human result before that episode, or after? It's been a while since I've seen season one, besides the final arc and the first episode.
But he for damn sure knows who they are.
Well yes we were meant to have the impression that he'd never tell. It however doesn't follow that he knows who they are or if any of the "Final Five" would even register any different then human.