I have a AE scanner and 6637 intake.
Assuming you have no boost leaks and the 38R is working correctly, stage 2 nozzles will have some additional off-throttle/tip-in transition smoke (especially in off boost conditions). However, the tuners should have accounted for it.
Does the HPO pump supply pressure as commanded? Does it smoke with both tuners files? Does it smoke in all files? Im assuming black smoke, but it wasn't said, so are we chasing a mechanical issue?
Take the truck out on a typical loop where you see it smoking and collect some live data. Export it to an excel spreadsheet and post the spreadsheet attachment. Describe for us what kind of driving you were doing (terrain, etc).