I have the same (similar?) problem. Using Auto Mode, pump A set to Alternating Gyre Mode (with positive and negative values) and pump B set to Anti-Syncronized with matching +/- values. Pump A always behaves as programmed, but pump B alternates on a ~5sec schedule using the programmed +/- values. I've done a factory reset on the controller thinking that there might be some conflicting program or odd entry in nvram, but the behavior persists.