Not sure if this is the answer to the OP problem. The FifoPi MA GPIO provides only 3.3V to GPIO pins 2 and 4. RPi standard GPIO is 5V on pins 2 and 4. Jumper J4 1-2 and 3-4 to share RPi power supply, leaving J5 unconnected. See step 4 in the Quick Start Guide of the manual.
