So we started to notice that after some projects, the right side of the Shapeoko is cutting slightly less deep than the left side. This only happens when the material is long and running past half the entire workspace of the table, to the right. I have checked levelness of table, parallelism of the gantry, waste board slats and all seems to be good by microns, but not sure if I checked everything. Any other checks needed that we may have overlooked?
See:
If that doesn’t address things, then check into the tool being deflected by climb vs. conventional milling — leave a roughing clearance and take a finishing pass (or passes, maybe add a “spring cut”).
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Have you flattened your spoilboard? Maybe it is slightly higher on the right side.
And are you sure that your material is flat?