I have a thought about this...

Have you verified timing to be correct? That what is being commanded is what is actually happening referencing crank angle, at RPM, I know without a dyno under load will be impossible to verify, but you can at least rev it in park and make sure that the actual timing follows commanded. I have seen a number of times where looking at commanded you'd think that the timing is far too advanced, but actual timing was not correct. There's a bunch of reasons for this, but starting with verifying correct timing is the place to start.