x,y and z axis problems on 3040T

[Neale]

One slightly odd thing I see in your settings. You appear to have "active low" selected for step and direction on all axes. That's fine for direction - change this and the machine reverses direction on that axis. However, "active low" for the step signal is unusual for the usual breakout boards/stepper drivers. The effect is that everything seems to work fine, but each time the machine changes direction on that axis you lose one step. Enough direction changes and the axis gradually seems to drift in one direction, fairly repeatably. Your test pieces don't seem to have that many direction changes compared with the overall error but as it's such an easy thing to change (and change back if it makes no difference) you might like to try it. I had this problem on the Z axis on my own machine; didn't notice a problem for simple profiling constant-depth cuts but when I started some complex 3D cutting, the cut depth gradually increased.

(Misread post - Kev's post says "dir active low", not "step". But worth checking that step is active high anyway.)