Have you ever verified that the threads on your ball screws are consistently giving you 1 mm of movement across the entire threaded length of the screw? I am not thinking about how you are moving the screw with a stepper motor, but turning one complete turn by hand with an index marker of some kind.
I can give it a shot if I can figure out how to get an index marker by which I can turn 1 rotation accurately.
I am using SG0801-100R140C3 KSS ballscrew. Datasheet. The company did accuracy tests before dispatch and it did come with a report. But I have been using it for few months now, so I am not sure if there could be some wear and tear.
Get it to move enough steps for (say) 50mm of movement out an back with a short pause when the direction changes. It should be back at the original position. If it is not tell us the amount of error for each run of (say) 10 tests.
Will try it out and let you know on Monday.