I had exactly the same problem. I solved it by milling of the bottom side of the aluminum ball screw nut mount on the Y axis. Easy for me cause I have another mill to do the work with. When I spoke with CNCFusion about this, they had seen it before, and told me that its not uncommon for the mill to be manufactured with too high of a mount. I actually still hear a bit of noise when I run my ballscrew to its extents and expect that I am wearing my ballnut out.
Scott...
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