So I took this to mean something along the lines of them betraying their logic process.
So in chess, when you see a certain opening sequence, or a certain gambit, you know your opponent has studied a certain type of style. I think it's the same here, where Kellhus finally sees the unmistakable gambit/logic path of Ishual, and there could only be one conclusion. I also remember he was quiet for a good long time, staring at the machine. Maybe he was doing his probability trance, hunting the threads of the Thousand Fold Thought that accounted for other Dunyain. Then he says not everyone can be saved, but amends it with 'this is a good thing.' Now why the shit would he say that? Besides the fact that he is constantly playing the prophet and saying cryptic shit to confuse and better possess people, I think, once he knew there were Dunyain in control of the Consult, he IMMEDIATELY knew how to defeat them, because he knows how they think, but he has been in the world for more than 20 years, and knows things they cannot fathom. He was precisely correct when he said 'I am the greater mystery here.'
Clever. Bastard.