Thats weird both of you have issues. I havent noticed anything like that with mine. I know Cobbs can be picky if you dont have the right mods to match the mapping...my friend has an STI with Cobb and custom intake..once he tuned it, the car didnt like it. He put his stock intake on and everything was fine. Although, I noticed Cure that you said once you did the Cobb the problem disappeared..strange.
As far as the coding and the faults go...I really doubt your coding is the culprit.
I noticed a couple of the faults have to do with the transmission...might just want to take the Cobb and the intake off and bring it in. Having a warranty is great..