I'm good friends with a couple of the guys that pioneered tuning. One of them said to me "Bill, I've never come across false knock that couldn't be tuned or mechanically fixed." Meaning, unless something is loose or rubbing, all knock can be found in the tune.
There are still plenty of tables that we can't see. We know that at best we have a couple of fueling tables that we are missing which is why we fudge our injector table etc to get close. DHP, Eddies Table Modifier, Tiny Tuner and HPT all clearly overlap a bit and have stuff that the next doesn't .....yet there is still a ton more that we don't have access to.
Likely you have a modifier table (probably visible) that is messing with you. PE, EGR, COT etc are common ones to mess with us on part throttle. Best way to combat this is to dig deeper into tuning, read until your eyes bleed at all the tuning forums available and test/check stuff. Sooner or later you will come across it and figure it out.