Normally the pickups add together. It doesn't seem likely that the pickups are out of phase, otherwise you'd be telling us about terrible hum.
Here's some stuff to test:
1. Make sure the humcancelling pickup is plugged in the middle connector on the preamp card.
2. Locate the two center trim pots on the backplate, these are the humbalance controls. Rotate them completely counter-clockwise. Now, listen to each pickup separately and both together. Confirm they are adding.
3. Follow the
humcancelling procedure from the FAQ.
Let us know how it goes.