I was too lazy to do it before, but solved the problem rather quickly.
The issue presents itself when adding these two lines to retroarch.cfg (/opt/retropie/configs/all/)
input_enable_hotkey_btn = "X"
input_exit_emulator_btn = "Y"
With X and Y buttons on the controller. It’s a button combination to exit the emulator. Taken from this guide https://supernintendopi.wordpress.com/
I guess that adding that option to exit emulators with a controller button combination somehow prevents SNESDev from using it’s button (in pin 11) to do the same thing.
But like I said before, in RetroPie 2.3 that problem doesn’t happen. I can exit with both the controller button combination and the SNESDev button in Pin 11 (with the same configuration).
It would be good to know if someone who is using the GPIO adapter has this same problem when adding those lines to retroarch.cfg.
I’ll contact the person that wrote that guide in case he wants to add a warning about this issue.