To give some specific background on my machine and configuration:
I am using colorfabb ngen (1.75mm) which seems to be incredibly well consistent on width. The esteps have been calibrated using the 100mm extrusion method which results in esteps of 817.7. It was further refined using the non-linear extrusion compensation the RepRapFirmware provides to 820, with additonal parameters that model the reduction in extrusion that comes when increasing extrusion speed. The last specific thing in configuration that might affect stuff is my use of pressure advance which was also configured.
The machine is a v6 extruder running a 600mm capricorn tube off of a Bondtech extruder.
I have never encountered the line width coming out of a 0.4mm nozzle using just an esteps calibration to result in a line of 0.4mm. My best slicing experience has been with s3d - it seemed to be pretty spot on with its assumption (0.48mm presently).
The only way to reduce this line down to 0.4mm seems to be adjusting the flow rate down to about 90% - which always seemed odd to me being that esteps should be properly calibrated.
When I print a hollow cube to test single wall thickness, I notice the first two layers put down aren't necessarily the greatest, so I might have to look there first.
I am really having trouble with this and would love to know if there is a better way, or there is something I am missing here. I do have two new 0.4mm nozzles (bought from MRRF last year in a 3 pack e3d had) and several other nozzles of various sizes.
Thank you very much for your reply.