Since it’s happening on both doors I think I would look at OD,and ODR to make sure it has enough time for a full travel. Those relays in the controller are a weak spot. I think that it counts encoder pulses from the limit that it’s leaving. If it doesn’t see the limits correctly it can’t count correctly. I know that I’ve been fooled before by the limit magnets with broken clamps or misaligned. Also with it happening on both sides I would want to check the supply voltages at the operator to make sure it’s sufficient.