I may be having a similar problem, maybe. Running 8 stack, and have checked ignition and injection (Noid lights and moving the injectors around), and all are working properly, in time, and in proper sequence, and valving is all proper and to specs. Yet have two cylinders that run cool (header tubes cool or just slightly warm). Further review indicates that the butterflies on those ITBs are closed more than the other 6 (barely perceptible), and appears to be verified by the observation that once I get off idle, into part throttle, those cool tubes get as hot as the other tubes. I've thought about drilling pin-holes in the butterflies, and then allow them to close completely, but am concerned that they may get sticky if I do that (plates wedging into the bores of the ITBs).
One other issue I also had on my self-learning system was a lot of backfiring at one time, which was progressively getting worse. Just out of curiosity I went to open loop to see what would happen (I felt I had the AFR pretty close to right by that time), and the backfiring disappeared. From that point on I manually adjusted the AFR, based on the wide-band readings.
How close have you matched the idle air flow for all the cylinders?