Dave,
I have had similar issues. The other guys are likely helping but I think there may be more to it than those changes. I have a blown 07 that kept showing random knock. A LOT of the occurrences were when I was coming OFF of the throttle. With the transition to the new Beta I don't have a great shot at hand but the one below should let you know what is happening to me and likely to you.
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What happens is that when mixed mode operation is enabled the prediction coefficients filter the airflow measurements/predictions. In my case you can see in the third panel of the log MAF Cyl Air and Cyl Air (unfortunately during this time the Beta didn't work for Fuel Cyl Air and VE Cyl Air) diverge during the transient. From the way the knock is occurring and the way the models are diverging it appears the blended model is too slow for a FI car. One of my undertakings during the Christmas break is to get these to match more closely and see what happens in terms of knock.
Again these guys are NOT telling you something wrong. I have tried as much of their suggested COAs as possible with a mixed bag of results. The closed loop integrator delay is evidently not available on our cars (I have already requested). I have tried to adjust the closed loop proportional airflow mode with some benefit but not to the knock issues I was seeing. I believe until the larger dynamic airflow issue is fixed the benefits of adjusting the amount of fuel required for closed loop fueling oscillation is insignificant. I believe the same is true for EOIT. BUT THESE GUYS ARE MUCH MORE EXPERIENCED THAN I AM.
I may just be spinning my wheels and may be doing the adjustments in those two areas incorrectly but the sometimes large differences between MAF measured airflow, VE airflow, Fuel Airflow, and Dynamic Airflow (these are the analogs to the cyl airmass values I chart) are the major cause of the issues - at least in my car.