The comparison between the two mean nothing without a data log of the vehicle running on each file. You saying the tables are dialed in doesn't mean...
I've run into this on the older trucks. The customer gave up before I ever found a solution. Another tuner advised to set everything back to Virtual...
Ok, I'll try to get a log soon. I was thinking that reducing timing at lower rpm would help with it but wanted to ask some more knowledgeable people...
Post a tune and data log. Standard procedure. Can't do anything but guess without both. You've been a member here for 4 years surely you've seen this...