Before you start swapping all the cables about - THE ERROR LIES IN THE CONSTANT VELOCITY, and is a combination of the narrow angle, speed, and relative low number of steps per unit.
If Constant Velocity is engaged, as an axis nears the end of its travel, the computer starts to calculate the next move, and actually implements it. Running the test piece, my axis was stopping some 30 thou short of the mark, and reversing, with constant velocity engaged. On Absolute Stop it ran the full distance.
I have 60 pulses per thousanth on my machine, so it was stopping some 1,800 pulses short of the mark. At a 4 degree angle, the difference in position of two lines at the 1800 mark is 125 - or 2 thou. Let us assume my old eyes are not as quick as they were and we were only 28thou short of the mark, then the distance between two lines at 4 degree would be 1.95 thou.
I do not know the precise method of calculating the CV "offsets", but if we have the old X position advancing up one path and the new X position advancing towards it on a new path, (at a known angle) then the Y distance between them can be calculated, based on the tangent of the angle, and if it exceeds the present Y position, then that is incremented.
The crunch comes as the two positions pass each other (and this only happens for acute angles), then in my example, Y may be incremented by one thou, but is short for the next thou, therefore nearly one thou is not incremented.
Now my machine has at least 6 true steps per thou, so (depending on the CV calcs) could be incremented by 1/6 thou, but if your steps per inch ar small, you will loose out.
Now Mach 3 will gaily carry on the second line, thinking it is on the correct y position ( which again could be being continuously calculated if this is at an angle to the axis) and when X reaches 0, the Y axis says I'm here - but it is a bit short. The same scenario happens to the X axis if the angle of the lines is rotated 90 degrees since the Y axis takes the lead.
I don't really want a discussion about the maths, since I have necessarily picked figures to help my explanation, but the fundamentals work with whatever angles etc, you pick - although the narrower the angle the worse it gets.
I think if you try all your tests in Absolute Stop mode, instead of CV mode then you will get accurate results - certainly more accurate than before - bearing in mind your relatively small number of steps per unit.
If you are in Absolute Stop mode then £$%&*&%$£