You my friend are experiencing the variable turbo's biggest downfall: inconsistent boost operation, usually due to sticky vanes and gummed up actuators. Best bet is to unhook the actuator from turbo clean it of diesel soot, residues, and debris, then re-install it. See if that shakes the turbo down and allows for it to boost properly. If not try running your truck un-tuned in stock calibration to see if the programming may be out of date,sync with your trucks original OEm calibration, or check for updates and download them from Superchips website. If none of this works, plan B would be to un-install the turbo and take it down and clean the vanes themselves of contamination. Actually the best way to clean them is to run the trucks EGT's past 1200 degress for short durations for as many times as you can throughout the day, this should act as a cleaner by burning off the residues inside the turbo. People who runn hooter tunes tend to have less problems with their turbo's when it comes to vanes sticking.
Hope this helps and god belss you fro owning a Powerstroke!!!