IHSS60-36-30 motor tuning/issues

Hello

I have question regarding motor tuning, did go trough numerous threads how to tune motors but didn't get too much information for it (due to different motor types)

I have same setup for all 3 axis/motors (IHSS60-36-30) (here is INI for one of them)
Motor switches are set to micro stepping 3200 (SW1-4) JMC manual  page 12
SW1  -  OFF
SW2  -  OFF
SW3  -  ON
SW4  -  ON
SW5  -  ON    (this was recommended to be ON)
SW6  -  OFF   (CW/CCW)

I have ordered dial indicator that can do 1inch for testing but till then I' looking how to improve this as much as I can

If you take a look on image
 
This is current values from milled example, RED values are measured via kaliper 
Big circles should be 20mm but measured are 18.88mm
Small circle in left corner should be 10mm but is 8.88mm
And square should be 30mm but it is 28.88mm

Not sure if this is step slipping or something else so any suggestion is more then welcome

I have checked Gcode and didn't find any G41/42 in so I don't think so that is the case

Backlash?

Was thinking the same but even if I push hard head in XY direction with dial I have (0.01mm/range 1mm) moves for a max 0.1 so that is not likely that is the problem

Look at actual tool diameter and compare it to tool diameter in CAM program.
Spindle run out will also cause a size problem.

So here is image with all important settingsTool I'm using is 5mm flat mill 3 flute (and is brand new, few cuts so wear is out of questions)I didn't see compensation at all in settings and Gcode there is no G41/42 so that is off also 
Attached milled part 

I know this sounds a bit wild/ like a longshot, but having measured ALL the dimensions at 1.12mm off, I would questions my metrology (if cutter comp, stock to leave and tooldiameter are ruled out).
Any scaling or ballscrew error in an axis should not result in the same absolute error over different distances. You mentioned that the square is off, are both of by 1.12mm? Some questions for the circles: Are they off the same way across both main axis (xy)?
The attached part looks ok, albeit the spindle trim may be off a bit and the cut shows some vibration.
Do you have a known 10mm reference (and be it an endmill) - does that truly measure around 10.00 with the same caliper? It got tricked by an offset caliper before, hence my question...

Share the settings for the 2d contour.
2d pocket is for roughing out the pocket. Finishing to size should be done with a 2d contour toolpath.
Since the difference is the same everywhere I expect a CAM issue.

Oher question, depth of the pocket, what was the difference there?.