At the end of “Tigh Me Up, Tigh Me Down” in s1 Head 6 comments to Baltar that everyone who undergoes his Cylon detector test passes as human regardless if the person is a human or Cylon. When Head 6 asks Baltar how the Cylon detector results on Ellen Tigh really turned out, Gaius says to Head 6 that “I will never tell”. This comment suggests that maybe Baltar secretly took the time to check Ellen’s true origin through his test samples, even though Baltar rigged his cylon detector to show the official results as human. And later in S3 after knowing the identities of the 6 active human-cylon models that have multiple copies and finding out about the missing final-five, Baltar might have come to the conclusion that Ellen Tigh was one of the final five Cylons. Of course everyone, except for Cavil and Boomer, assumed Ellen died on New Caprica, and there was still wiggle room for Baltar to speculate that he was also one of the final five Cylons.