Another reason that I can think of might be that the SNES sockets are still connected to the original SNES main board (at least it seems so from the pictures). The ICs on the main board could interfere with the signals from the ControlBlock.
You could test that by changing the configuration of the ControlBlock to arcade, using a GND connected wire to simulate button presses by momentarily connecting it with an arbitrary pin of the ControlBlock that is currently not connected with the SNES main board. You should see that simulated button press as “ON” in with the tool jstest. That is also another way for confirming the correct functionality of the ControlBlock BTW.
Or you could just disconnect the SNES sockets from the SNES main board.