If I recall correctly, doesn't Achamian think it's the Spires? I mean, we can't blame the guy really, he is kind of distracted by his day job (that his day job is to perceive threat is probably another Bakker nod to bias ).

Though, as you said, maybe later Achamian was like "ah, shit, Kellhus, I saw a Synthese" and Kellhus said "yes, this is a good thing."

He says "his mind was racing, was this a consult attack? or just scarlet spires mischeif?" 

compare to when Inrau sees a synthese:

"OH FUCK OH FUCK OH FUCK WHAT DO I DO WHAT DO I DO PLEASE REMEMBER A SPELL PLEASE REMEMBER A SPELL!" Hiya, punches through someones chest!

That is an appropriate reaction to spotting a sorcerous bird.

Doesn't it seem like achamian should be more concerned about catching a glimpse of a "sorcerous bird?" Even Inrau recognized the synthese as consult when he saw it, even if he didn't know what a synthese was. It bothers me that Achamian didn't freak the fuck out when he saw this.

Also, later in chapter 12, as Aurang is having an (epic) conversation with Kelhus, Kelhus states that Achamian had discussed snythese with him, indicating Achamian has enough information about synthese to have known what it was. I think glimpsing a sorcerous bird should have set off more alarms, with greater urgency for Achamian. Then again, maybe it did, as Kelhus sets the trap for the skin spy.

Chapter 12 is immense. 

Hello. I read the first book in 2004, and have never read any of them twice. I barely have any clue what is happening each time a book is released.