Have you measured the actual case capacity, length of the case if not trimmed, bullets for their weight and length, and actual OAL? These are factors that will influence the pressure predicted.
An example would be:
Using defaults, QL says my .22-250, using 36 grains IMR-4895 and a 50 grain BlitzKing, seated to default OAL would have 55,368 psi pressure and 3850 fps velocity.
Actual measurements of components are:
Case capacity-default says 43.49, mine are 45.2
OAL length-default says 2.350" , I can go 2.468" (.010 off lands).
Bullet measurements were:
Default--.786", 50 grains.
Actual--.785", 50 grains. (very rare for one to weigh exactly what the manufacturer says).
This resulted in a QL prediction of 48,458 psi and 3724 fps. Which, by the way, was only -13 fps off, and a quick tweak of Ba brought this in line.