The controller I am using, NX-Max 4-axis ethernet, was made by a local enterprise. I bought it a couple of years back and I was surprised to learn that they do not make the card anymore and give little to none support to it. To be honest, when I called them, I got no good answers and a lot of arrogance. Unfortunately it took me too long to build this machine but I thought it would br nice to have a top of the line controller.. but now I am on my own regarding this component. Although I do not think the controller as much as a suspect, but I wanted to mention the lack of support in case some doubt about it arises. Cheers!

The drivers are connected like this, according to the NX-800 documentation and the motors definition in mach3.

Are you using shielded cable to the motors and step/dir grounded at one end only?

For the moment ignore the steps/per as it has no bearing on your problem.

Your problem is missed steps or extra steps.  This can be noise on the motor cables from power lines being too close or on the step/dir lines or even a dodgy power supply.  it may be you need a filter on the AC input or a different motor PSU for testing.

Once the cut design is starting and finishing in the correct place then worry about fine tuning the steps/per.

Edit your g-code so the last move is the same position as the first move so you can see if its back to the right place.

X axis motor cable and spindle are shielded from the motors to the front plate conector. Y cables are shielded for the most part, going "comando" only half meter to the front plate conector. Connections inside the electronics enclosure (which right now is only a base where the parts are screwed to), are normal wiring. I changed most of the wires to not cross any power supply lines, but it is hard to say if there is enough distance to avoid any noise. The ethernet cable for both notebook and controller are CAT6 from Furukawa, so I don´t think they are prone to pick up noise.  After changing positions of cables and AC feed lines, I run a small program in the air (meaning spindle off and no actual milling), marked the zero position and bam... there is the same deviation to X and Y axises.  The ceiling is quite low on this part of the woodshop where I have the cnc installed and illumination is from cheap Chinese led lamps... Tried to leave everything turned off. Run the program once more... same results.  At this point it is worth mentioning that the deviation is pretty consistent at -5mm for both X and Y.  Checked the little gcode and there is already a line sending it to x0 y0 at the end of the program.

Did I mention that my kernel speed is set to 100Khz? And pulse and dir are 5us?

Hi,
if you are using an Ethernet connected motion  controller then the kernel speed is irrelevant, the kernel
speed applies to Machs parallel port.

I would disable or even remove the parallel port driver entirely, you don't need it and its a CPU hog should it be running
even when you don't want it.

Craig