Swap the cable connection from one of the small boards to the other. If the problem follows the connector, it's a cable, or interface issue. If the new board doesn't work, even with the cable from the other axis plugged into it, it's a bum board. You may just be having bad luck with the small boards, but also make sure there isn't anything, like a short to neighboring wires, that is causing the boards to fry. Also check the power going to the trackball and make sure it is what it should be, and make sure you are grounded when handling the PCB's. Cold weather makes for dry air and more possible complications from stray static discharge.
RandyT