RetroPie on RaspberryPi 4: Handful of GPIO pins not readable in config

[SomehowAdultMan]

Hi all

Here is a description of my setup:
Pi Model: Raspberry Pi 4, 8Gb
Power supply: The wall-plug that came in the box
RetroPie version: RetroPie Buster 4.8 2022.03.13 (under BerryBoot)
USB devices: Generic keyboard and generic mouse
Controller: Buttons connected to GPIO pins

I'm using GPIOnext to enable buttons being connected to the GPIO pins.
For a couple weeks we've had the buttons connected to the pins listed below, but we recently decided to add two more buttons (we have plenty of GPIO pins after all) - but we can't get GPIOnext to react appropriately to the buttons being pressed while connected to any of the remaining GPIO pins.

When running GPIOnext config the old buttons are registered as expected - but if we try to add any button to any new pin there is seemingly no reaction at all when pressing the corresponding button. There is one exception to his: If we connect a new button to pin 36 (GPIO16) GPIOnext does respond saying that a button now is set to that pin (as we want) but then get stuck with the text "release all buttons". At this point we cannot go further with the configuration no matter what we press (except ctrl+c to cancel the configurarion).

To run some diagnostics I've made two Python scripts: One to toggle HIGH/LOW on specific pins, so I can see that an LED connected to that pin works; And one to react to a button connected to a specific pin being pressed. All the GPIO pins passed these tests - the LED can be made to blink with any of the GPIO pins and the script will print "A button was pressed on pin X" when I press a button connected to pin X.

We are currently running RetroPie 4.8 under BerryBoot, but the same issue was present when we were running a different RetroPie 4.8 image (RetroPie Buster 4.8 4_400).

The following pins are connected to buttons/joystick and work flawlessly ("functional pins"):
7 (GPIO4)
8 (GPIO14)
10 (GPIO15)
11 (GPIO17)
12 (GPIO18)
13 (GPIO27)
15 (GPIO22)
16 (GPIO23)
19 (GPIO10)
37 (GPIO26)

What might be the reason that I cannot add any buttons to the other pins (for example pin 3, 5, 18, 22, 24, 26, 32, 36, 38 or 40 ("unfunctional pins"))?

There doesn't seem to be any issue with the button themselves as we have tried a handful of them on the unfunctional pins with the same results, though the same buttons work on the functional pins. If there is any form of hardware fault I am confused as to why my script-tests all passed with reading and writing to/from the unfunctional pins. Any help in resolving this is appreciated.