I think that you are right that is an issue and when we fix that things will be better, but mine does that too 
I think that is the kind of thing which takes us from a 0.8 calibration to a 0.7 but I don’t think that could take us to 0.02.
I am going to work on trying to make the calibration work with just three belts (I think it is possible) and then run the numbers for each set of three belts and see if we can track the issue to just one arm.
I was also wondering (I literally had a dream about your calibration issues last night 
) if it might be worth fully wiping the firmware and starting fresh in case there is some funky configuration bug.
If you have a chance and a USB cable, can you run the “Full Install.bat” in this folder with the USB cable plugged in and the machine powered on (It needs the power-supply connected to program)?
That will fully erase your board and reset everything to factory defaults.
Edit: File was too large to upload, working on it
Edit2: Here we go: Full Install — Maslow