knock can be caused by MANY things -- and yes, thats what was happening when the cel flashed. It could have been the gas, the weather was colder or warmer, or its just too aggressive.
The UTEC pulls timing for a few RPMS, that was the lag in power you felt. Its very sensitive and thats a good thing. It will usually pull timing faster than the stock ECU will. If it happens rarely, thats pretty much to be expected. If it happens often you need to tone it down in the areas you are having problems. Usually it just means dropping boost slightly, or taking out a point of timing.