Rob, I'm glad to see you toughed it out and let Axiom's excellent service deal with the problems you were having.
It really is a phenomenal amp and IMO has set a new benchmark performance for Class D amps. I've had a couple of chats with Tom about the Audessey problem. Making a long discussion short it has to do with how the new program in the Integra 9.8 flucuates higher amounts of voltage which prompts a safety shutdown. Its hard to say whether its the fault of the Audessey or Axiom's safety precautions. Other folks like ihifi (John) have use the Audessey in the Onkyo 905 without problem.
In any event I've always felt the Audessey programs were not very good and very overhyped so I never use them.