Please check the machine mechanically. Per the machine operating checklist: Machine operating checklist , the basic points of adjustment for a machine are:
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Pulley set screws — verify that these are in-place and secure — for further details on checking them on a Shapeoko 3 see: http://docs.carbide3d.com/shapeoko-faq/shapeoko-3-how-to-check-the-pulley-set-screws/ — be sure to check all axes/pulleys (including Z on machines w/ belt-drive Z-axis, for an HDZ, check both coupler screws).
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(for the SO3/4, X- and Y-axes) V wheels / eccentric nuts: Tightening Eccentric Nuts - Carbide 3D
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(for the Pro, and SO4 Z-axis) Lubrication of the linear rails: CNC Machine Maintenance
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(for HDZs, and HDMs, and SO5 Pros) check that couplers between the motor and ball screw are secure, for the SO5 check that the DAC which transfers the rotary motion of the ball screw to linear machine motion is secure on the carriage/gantry
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Belt tension (see the relevant step in your instruction manual, e.g., Getting Started with Carbide Machines) Note that the X-axis motor is held in place on standoffs and if those bolts are loose this can cause belt tension issues. Also, belt tension for the Y-axis stepper motors needs to be even/equivalent on each side — a significant difference can cause skipping on one side eventually resulting in lost steps on both. Measuring belt tension, squaring and calibration
Although on the Shapeoko 3, this is a good video overview on setup:
Ensure that all screws are in place and secure, esp. on the linear rails on a Pro.
Also verify that all wiring is in good condition and all connectors are secure, and that all wiring leading into connectors are properly in place.
If you don’t find anything obvious to address, let us know at support@carbide3d.com — mention that you’ve seen the above mechanical checklist, and send us the .c2d file, step-by-step notes on how you are securing your stock and setting zero relative to it and managing all tool changes, and a photo showing your setup with the stock still clamped in place.