Does the 3D preview match?
If not, the problem is likely a mechanical or electrical issue.
Make sure that nothing is interfering w/ machine movement — if all is good on that front, per the machine operating checklist: Machine operating checklist , the basic points of adjustment for a machine are:
- 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).
- (for the SO3/4, X- and Y-axes) V wheels / eccentric nuts: Tightening Eccentric Nuts - Carbide 3D
- (for the Pro, and SO4 Z-axis) Lubrication of the linear rails: Getting Started with Carbide Machines
- 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
Electrical issues are usually accompanied w/ awful noises — make sure that all connectors and wiring are in good condition and secure, and make sure that the wiring leading to and exiting from connectors, and the connectors themselves are secured so that they will not move and cause stress to the wiring: