Well, it was the Six in Baltars head that brought it up to him later on after the "vision." Regardless of how he actually had the vision, she still brought it up to him later on. I still think there is more to SiBH than just a hallucination. Just because a MRI or what ever they did to Baltar couldn't find a "chip" doesn't mean there isn't something of that nature there. If Sharon can hook up a fiber-optic cabel in her arm but still be indistinguishable as a Human, then the Cylons must use some form of advanced bio technology that can't be easily noticed. Either way there has been too much that happened to Baltar, in regards to Six, that just can't be written off as coincidence.
I agree that Six never told him of the Baby incident, just that the cylons have this great capacity for hypocracy. Sharon, was the main source of this in season 2 when she copped attitude to people who where misstrustful of her, but the SiBH has also done this to Baltar on several occations but that could easily be designed to get him on her side.
Chris