I'm not sure that this is your issue but check it out. I had the exact same problem when I built my first home brew. I used a Rong Fu 31 with servos and the flashcut boxes.
My first part had a flat on the top of a circle just like yours. It took me about 30 min to figure out the head wasn't fully tight on the column.
Could also be backlash in the y axis, either at the nut or at the pillow block (or in the software compensation).
I hope thats your problem, easy fix.