Have you measured your filament’s exact diameter? Sometimes filament that’s advertised as 1.75mm can actually be as small as 1.7, which would cause under extrusion.
If you determine the diameter is smaller, this can be changed in Simplify 3D.
I actually don’t see any under extrusion in your photos, however. The blue cube shows some layer shifting (can be fixed by printing slower and tightening belts), while the black print looks quite nice other than some stringing.