This is on a servo system not a stepper?
Is the axis smooth to turn over manually (with the power off). I'm thinking of a bad bearing, or a bent shaft which would produce a tight spot.
Other than that, I'd suspect a defective encoder, bad cable, bad shield, or perhaps a loose coupling between motor and encoder which would create a spike when position is momentarily discerned by the controller to have strayed, which creates a large 'position error' which the servo attempts to recover from. It happens so quickly that it appears as a bump.
It might even be a bad winding on the motor.
You should be able to isolate the problem between amp, motor, and cable by selective swapping of components. Remember to keep the motor and encoder combinations together to prevent runaway, or the safest method, disconnect the motors from the machine for testing.