I once had a problem with one of the stepper motors on my 3D printer that was due to a bad connection inside of the connector that connects the control board to the stepper motor. It would have taken me forever to figure that out myself, but the support staff at the manufacturer was familiar with the issue, so they suggested it as a root cause immediately after I described the symptom to them. They told me "t
he issue you're having stems from one of our early manufacturing partners using the wrong crimp diameter on those motor pins" and then described a procedure to fix a connection inside the connector that plugged the stepper motor into the control board.
Sure enough, I fixed the connection inside the connector (removed wire and pin from connector, soldered wire onto pin, reinserted it into connector) and my problem was solved. Now I'm not suggesting that the problem with the Shapeoko has the same cause, but just wanted to share my experience that sometimes even if it seems like the connector is tight, the problem can still be a bad connection.