Reset the base FP and let us know what happens.
Once base FP is set the FP should decrease by 1 PSI for every 2 In./Hg. of vaccum applied to the regulator. For example, at 20 In./Hg. of vacuum at idle you should see about 30 PSI of FP.
When boost is applied to the FPR the FP should rise at a 1:1 ratio... in other words for evry pound of boost the FP should increase above the base FP by 1 PSI. If your truck makes 12 PSI of boost at WOT then you should see approximately 52 PSI of FP at WOT.
I don't think the pressure differential between your gauges is due to the improperly set base FP though, that may still be a gauge reading inaccurately.