I believe I finally have a design and two sets of test GCode that demonstrate my issue in a testable manner. The design is still like this
[image: Screenshot, no longer available]
A design file may be found here
https://dl.dropboxusercontent.com/u/50261731/ShapeOko%20Test4/ShapeOko_Diagonal_Test_4_in_mm.dxf
In this design, the diagonals are spaced 0.1".
When run on my shapeOko, I found that the cut width of the lines should be 0.06" or a bit more to make the error better viewable.
One set of GCode, Optimized GCode, is found here.
https://dl.dropboxusercontent.com/u/50261731/ShapeOko%20Test4/ShapeOko_Diagonal_Test_4_in_mmOptY.nc
This set of GCode seeks to minimize the total tool path for the job and cuts the red line above in sequence, clockwise from the lower left corner.
This Optimized GCode shows offset diagonals when compared to the free drawn adjacent diagonals.
The second set of GCode is non-Optimized and found here
https://dl.dropboxusercontent.com/u/50261731/ShapeOko%20Test4/ShapeOko_Diagonal_Test_4_in_mmOptN.nc
With the optimizer turned off, the GCode generator (in QCADCAM 3.6.4) appears to cut the paths in the order they are drawn by the CAD system, and cuts from the start of the path to the end of the path, as defined in the CAD world. If you run a GCode simulation on this file, you will see that every diagonal and horizontal or vertical path are cut separately.
The non-optimized GCode runs do not show any offset, as seen with the optimzed code.
I captured the image below on my flatbed scanner then Gimp'ed to improve contrast.
Note that the non-optimized runs(right side) appear to be cut with slightly wider lines, most likely due to material surface variation.
The wider cut actually acts as a visual difference "enhancer", and still you see no perceptible variation between the diagonals.
I ran each set of code three times, once with $ja=200,000, again with $ja = 750,000 and finally with $ja=2,000,000. I perceive minor improvement as $ja increases
[image: Test4-mm-6 runs_2_Summary.png, no longer available]
You may find it easier to view this in a downloaded window
https://dl.dropboxusercontent.com/u/50261731/ShapeOko%20Test4/Test4-mm-6%20runs_2_Summary.png
The config file for these runs is found here
https://dl.dropboxusercontent.com/u/50261731/ShapeOko%20Test4/2014-04-03_14.00.05-tinyg.conf
Root cause remains a mystery or work in progress.
I have not tried the latest edge FW, 421.06.
I am about to disassemble and expand my ShapeOko a bit.
I will re-run this set again to see if a possible mechanical cause is implicated.