It’s the on-board gyros that are probably causing the slight acceleration. They impart their own torsion field as they spin.
From the article:
The five other flybys involved flights whose incoming and outgoing trajectories were asymmetrical with each other in terms of their orientation with Earth's equator, which "suggests that the anomaly is related to Earth's rotation," Anderson told the Times Online. As to whether these new anomalies are linked with the Pioneer anomaly, "I would be very surprised if we have discovered two independent spacecraft anomalies," Anderson told SPACE.com. "I suspect they are connected, but I really do not know."