I admit I could be wrong in my recollection though. Maybe we are supposed to think that Baltar's test was real indeed. In which case, we have a different contradiction: Why didn't it flag Tigh, Tyrol and Tory? (Can't remember if Anders was with the fleet at this point) I mean, if (1) the test is real and (2) those three are supposed to be "Cylons"?
Baltar lied about the results, but the test was real, and worked exactly as planned.
The Final Five are different from other Cylons, in ways both obvious (only one copy known of each, outside of all existing Cylon heirarchy) and unknown (why were the other Cylons forbidden to ask or think about them?)
Baltar lied about Boomer. He never gave any indication of knowing that the others were Cylons. Nor did the Six in his head give him any indication that something funky was going on.
They're grasping at straws now. Seriously. Glad I'm catching up on SG1 reruns and that I only have a day and a half for Dr. Who.
Ok, I'll have to take your word for it. This wasn't obvious to me watching the show, but admittedly maybe I missed a key line.
This still leaves the question as to why it failed to catch Tigh/Tory/Tyrol.
The Final Five are different from other Cylons, in ways both obvious (only one copy known of each, outside of all existing Cylon heirarchy)
"only one copy" vs. "many copies" is not really a biological difference. Let's say you meet me and think "person". Later, you find out I have a twin: does this make me "different"? From people with no twins? Far as we can tell, D'Anna now has no extant clones ("copies") whatsoever; does this suddenly make her "like the Final Five" and "different from the non-Final Five"? Of course not.
and unknown (why were the other Cylons forbidden to ask or think about them?)
Neither is this a biological difference.
What you really seem to be saying here is that their role/function is different from that of the other "Cylons". Yes, of course. The reason for that is largely dramatic and (I suspect) economic: the TV show hadn't 'revealed' five models, probably hadn't signed any actors to play them, but were nearing having to wind-up the story arc, and so they cooked up this bogus mysticism and drama about "The Final Five". In other words the Five have been given "different" roles for purely extraneous reasons of plotting and drama and casting. Which is precisely the point I was trying to make, of course.
It remains a mystery how they are or could be "different" biologically. And thus, why Baltar's test - if it was real - failed to catch them. This remains a mystery because, of course, the whole "Final Five" stuff was cooked up later, and the writers didn't bother too hard about consistency. Which, again, is precisely my point.