B and X button give same output

[Scaryfish]

I've just finished my Freeplay Zero build and have a bit of an unusual problem. I think it's probably just a config issue but I can't figure it out.

I'm using the "silicone rubber pad" style of button install, so there were two new holes drilled, above and below the existing A and B button holes. 

When I try to configure the controller, all of the buttons register presses, but the "south" button gives the same output as the "north" button, input 3.

I'm sure it's not a physical problem - I don't see how pressing the "north" button could be actually contacting the "south" contacts without also pressing the "east" and "west" ones. I suspect it's a config file somewhere that has those two buttons giving the same output.

I've had a look in /opt/retropie/configs/all/retroarch-joypads/GPIO Controller 1.cfg 
As far as I can tell, it looks as it should. At least it has different button ids for a, b, x and y.

Code:

input_device = "GPIO Controller 1"
input_driver = "udev"
input_l_btn = "4"
input_load_state_btn = "4"
input_start_btn = "7"
input_exit_emulator_btn = "7"
input_down_axis = "+1"
input_r_btn = "5"
input_save_state_btn = "5"
input_right_axis = "+0"
input_state_slot_increase_axis = "+0"
input_select_btn = "6"
input_left_axis = "-0"
input_state_slot_decrease_axis = "-0"
input_up_axis = "-1"
input_a_btn = "0"
input_b_btn = "1"
input_reset_btn = "3"
input_enable_hotkey_btn = "8"
input_y_btn = "3"
input_x_btn = "2"

Is there another GPIO Controller config file somewhere?