There's no real reason to suppose that the final five were physically special; it was their technology and seemingly their genetic pool that created the significant seven models. Also, Baltar's cylon detector (mark two) works by simply identifying synthetic samples from natural ones, or so he tells Adama. Barring a substantial plot hole, a false negative result or a completely out-of-character decision to sabotage the test and let potentially crucial information pass by him, Baltar knew perfectly well that Ellen was a cylon.
It's probably just a plot hole, though.
Conveniently, the one moment when this information would've been most useful--Three's hostage situation in "Revelations"--had Baltar as one of the hostages, so he couldn't tell Adama who the Cylons in his fleet were.
At a minimum, Baltar should've known that Ellen and Saul were Cylons, maybe Tyrol, but not Tory or Anders. It depends on who all was tested, and presumably Adama's entire command staff were.