05 EGR codes from tune

My 2005 6.0 had been tuned in the past with SCT, when it was still able to disable the EGR. My system is intact and I have checked to make sure it is clean and functional. When I switched to HP for tuning, I lost the ability to disable the EGR and now am getting a code for EGR insufficient flow pretty much every time I drive it. I can clear the code and it will not show back up for the rest of the drive cycle but I literally have to clear the code EVERY drive cycle.
I'm pretty sure this is a function of the tune but not sure WHERE and what to adjust to try and clear it up. Not asking or trying to defeat or turn off system. Just need to figure out where to adjust parameters for the EGR to read sufficient flow. Truck runs great, just annoying with the code. Would I be better off not having the code report at all and disable the SES?