N64 Controller working in Retropie but not in games.

[Deathl1ke]

Hello,

I have a raspberry pi 3 running retropie 4.1. I'm using a mayflash controller adapter with the original N64 controller. I've configured the controller and everything works fine in the menus but as soon as I load up a ROM, the button layout is really weird (A is start or sometimes Z is start) and nothing is what I set it to. There's a thread with almost this exact same issue and I've tried switching to the LR-Mupen64plus emulator as I read that has a different controller config but that did not work for me as the controller wasn't even registering any button input and the performance was abysmal.

Pi Model or other hardware: Raspberry Pi 3 Model B
Power Supply used: 2Amp 5.3V
RetroPie Version Used: 4.1
Built From: Pre-made SD Image on the Retropie website
USB Devices connected: Mayflash Dual Controller Adapter
Controller used: Original N64 controller
Error messages received:
Log found in /dev/shm/runcommand.log (if relevant):
Guide used: (Mention if you followed a guide) Tried setting it up with https://github.com/retropie/retropie-setup/wiki/Nintendo-64 but maybe I'm not tech savvy enough.
File: (File with issue - with FULL path)
Emulator: (Name of emulator - if applicable) Mupen64plus but also tried LR-Mupen64plus
Attachment of config files: (PLEASE USE PASTEBIN.COM FOR LARGE LOGS)
How to replicate the problem:

I've spent almost 2 days looking around on google and trying various things and looking at youtube videos and I just can't seem to get it >< if somebody can point me in the right direction I would be so appreciative.