My concern is if he was, is the fueling in the ECM tune matching it...?
I doubt in Nicks tuning its wrong as he has some pretty good guys working on his tunes, but some will raise shift points and on the bottom of next gear, they forget to adjust fueling in the ecm tune to compensate for it and loose quite a bit of rail pressure. Sounds pretty much a fuel issue to me, just need to track it down.
Visually is it cleaning up pretty good? Does the truck fall down on shifts pretty hard or not pick up going into next gear in the first 1/8th? I'd take good looks at pressure at the early shifts. We can loose 2-3 tenths in shifting alone at low 12s..