E3D V6 underextruding always?
Major factors affecting extrusion:


Nozzle diameter
Extrusion ratio
Extrusion stepper calibration
Filament actual diameter
Extrusion width setting
Nozzle temperature


According to the photos, temperature is acceptable (may be a bit high, but it is not a problem in this case). Extrusion ratio is 1 and should not be changed in normal operation. Extrusion width is often set to auto but sometimes calibrating it gives better results in slic3r. If stepper is calibrated properly, then I would check for nozzle and filament diameters. For nozzle it should be enough to verify that 0.4 bit fits in and 0.5 doesn't. Filament can be measured by digital caliper. Difference between 1.75 and 1.73mm may have significant difference resulting in under-extrusion.