Hello, I have not setup N64 in a while, but I remember there being an “AutoConfig” file of some sort that would overwrite my manual changes.
I was able to update that file and it no longer imposes it’s will upon my setup. That may or may not apply to your GPIO setup but it is worth a look.
EDIT: Totally missed your reference to that file. Sorry. I do believe that is the culprit though...