We are getting bogged down here.
I will return to the point I made in my first (and only) post - which has been , to a certain extent, picked up by Brett.
I have not seen yet where you have calculated your steps per inch movement for your axis. I know you say you have done thousands of tests til you are sure it is accurate, but any measurement is suspect.
I have said it before many times, and I will say this again - not because I am stubborn (which I am) - but becasue it is a mathmatical fact - steps per unit should be calculated not measured..
Can you please tell me what result you arrived at when you calculated your steps per inch.
I do not know how many steps per inch you arrived at - but if this is out, it will not show up on moving a table up and back. Your measurement could be in handspans - but as long as you went up three handspans, and then back, you would arrive at where you started.
If you have a relatively small number of steps per unit, your error, if you have made one, will be greater, although if these are clock parts I would have thought you would have a large steps per inch for accuracy.
When moving two axis together, the axis moving furthest takes the lead, and moves at what speed is set. The second axis has to move as per the tangent of the first, not often a precise number, at whatever speed is set, and the figures for the steps the computer puts out are necessarily truncated. Again, if you have made mistakes, then the calculation of tangent is being made on a mistake, which again, must produce a larger mistake.
I do not really want to get involved in this post, becasue I have laboured these points often in the past, but I would like to see some calculations for your steps per inch (for both axis, if not identical) and then perhaps we can pursue Bretts worry about your backlash.
In the post you quoted an error of 0.00035 - am I correct - are we talking about 1/3 of a thousanth of an inch. I do not have kit that can measure that accurately, and I do not think my hands and eyes could use it if I had.
They only problem - going back to your steps per unit - if you are looking at errors that small, you are looking at a small number of steps
My steps per unit is 60,000 per inch, actually 6,000 if you ignore the Gecko microsteps - i.e. 6 per thousand - so 1/3 of a thousanth is two steps. If you have fewer steps per than that, one step could be 1/2 a thou.
Have you tried, on your motor driver lines, ticking "low active" for steps and direction (or vica versa if they are already on active low) . For your breakout board, it may be that the first step is missed if your output lines are artificially held in one state or another.