Have you checked the X and Y axis to see if they also have this issue?
I haven't seen any problem with the other two axes but I also didn't see a problem with the Z until doing a lithophane. I have done other 3d carvings with no noticeable deviation in the Z.
So to answer your question, No, I have not checked the X and Y but only because I have no idea how to. I've been trying to come up with a way to generate the type of movement the litho causes in the Z, in the other two axes, but I am not having any luck there. I will say that I changed the pulse width on all motors though, just because I'm guessing it may be effecting all of them. I also do not think there was any difference between going to 20us as opposed to 10us. I will have to double check this tonight but I think the amount of change that the 10us pulse made was the same as the 20us pulse.
Please send me a profile package, and if possible a GCode file that causes this problem (the smaller the better).
As far as the file, I've actual been using 3 different files with the same results from all of them. I'll send the one I used last night but it is a lithophane, so it won't be 'very' small.
Also, I guess I forgot to mention that I did swap the motor outputs, as you asked, with no difference. I used the Y output, with the Z cable. So the only thing common at that point was the motor and cable but I have previously replaced them individually with no improvement.