My guess is you are experiencing the anti-skid adjusting to the variation of pressure that you are applying when you brake manually. The auto-brake has a more controlled or constant rate of deceleration as in comparison to the more varied brake modulation that you would experience with manual brakes. With each modulation of brake pressure, the anti-skid has to readjust. Large and varying brake modulations can cause what may be described as a 'jerking motion,' as the anti skid readjusts pressure quickly.
This is only one explanation based on my experience. You should check the tech log for any history and consult maintenance if the problem seems more pronounced. Brake or tyre problems will generally cause the aircraft to weave or yaw to a particular side. The FCTM describes brake and tyre issues alongside their associated problems in the non-normal section.