I have ballscrews with anti backlash nuts on all axis'. Why I thought I needed backlash compensation is beyond me.
I never used it before, but like I said I thought maybe it was my solution to circles coming out slightly square so that's why I enabled it prior to me encountering my lost steps.
Maybe the circle thing is a CV issue. I have no troubles with any complex designs or square pockets but that is a topic for another day.
Thanks again!