@bfenty if it is activating the unused c buttons try mapping those c buttons to non existing button numbers. (Like 20 and 21)

This is what RetroLink and Retro-Bit N64 USB adapters do, because they don't adhere to the USB HID standard.

I posted a couple of possible userspace drivers here https://www.reddit.com/r/RetroPie/comments/53bt1d/retrobit_aka_retrolink_usb_adapter_driver/ but nobody has reported trying them out yet.

Alternately, get a different adapter. I have had success with one which looks like this: http://i.imgur.com/cC8iegW.jpg

@RetroPieNerd that would be awesome! Everything is just better, less sound bugs, less texture bugs, in general just look cleaner. Project 64 1.6 is an improvement on mupen but 1.7 really is the best one out there, just harder to find, even with google. 2.0 or higher is/has malware though. So 1.7 is the way to go.

While trying to be helpful, the above posts were not specific enough.

Using hints from the config files here:
/opt/retropie/configs/n64/InputAutoCfg.ini
/opt/retropie/configs/all/retroarch-joypads/WishTechnologiesAdaptoid.cfg

And the official documentation from both mupen64 and retroarch, I managed to create a configuration specific to the N64 controller with adaptoid USB<->N64.

(EDIT: The below confusion caused by one simple issue. One cannot restart emulation station to reload the /opt/retropie/configs/all/retroarch-joypads/, one has to restart the entire RPi!!! What a bug D:)
There is some confusion for me that I'm trying to work out. I set the save/load state, but somehow load state on button "12" and in the mupen config it's "DPad L = button(12)", yet start+C-left will load state... Weird stuff all around.

In WishTechnologiesAdaptoid.cfg:
#Start button
input_start_btn = "8"
#Start is now the "hotkey"
input_enable_hotkey_btn = "8"
#Left shoulder "L"
input_l2_btn = "6"
#Start (hotkey) + Left-Shoulder will exit the emulator
input_exit_emulator_btn = "6"

Full adaptoid config in /opt/retropie/configs/n64/InputAutoCfg.ini
I was using this to reference what button is what for the above changes. By default from the previously linked config, it had some issues, such as A button was C-down, C-down didn't do anything.

; Wish Technologies Adaptoid_START
[Wish Technologies Adaptoid]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
C Button D = button(1)
C Button L = button(4)
Z Trig = button(9)
Start = button(8)
Y Axis = axis(1-,1+)
DPad U = button(10)
C Button U = button(5)
B Button = button(3)
A Button = button(0)
DPad D = button(11)
X Axis = axis(0-,0+)
R Trig = button(7)
DPad R = button(13)
DPad L = button(12)
C Button R = button(2)
L Trig = button(6)
; Wish Technologies Adaptoid_END

Side note, I wanted to make sure keyboard and other controllers are disabled. I have some USB SNES style controllers, but I don't want them working with the N64 emulator.

In /opt/retropie/configs/n64/InputAutoCfg.ini
Find the "plugged" option for keyboard and other controllers you don't want to run in the N64 emulator, and change "plugged" from "True" to "False"
; Keyboard_START
[Keyboard]
plugged = False

#My case has these other USB controllers configured:
; 2Axes 11Keys Game Pad_START
[2Axes 11Keys Game Pad]
plugged = False

@thord I did what you said and the problem persists. I'm on my original install of 4.0.2 on a Pi 3b. Should I try to update all installed packages? Why am I asking? That's what I'm going to try anyway. With this problem I've also noticed that my iclever bluetooth, mini keyboard will function during a dreamcast game, but only in the command prompt (which displays along with the game for glitchy reasons I presume). The game won't respond to the keyboard after idle. I might try plugging a usb ibuffalo snes pad. Wonder if it works to plug it in after the idle glitch. I also wonder if my iclever keyboard, bluetooth dongle is interfering with the on chip bluetooth.

Perhaps the .sra file is made by one emulator and .srm by the other..I'll have to check tomorrow

You don't list which emulator. You can switch to ones with hires resolution set in runcommand - https://github.com/retropie/retropie-setup/wiki/runcommand but some games will be slower.

By default we use the original N64 resolution which was low res, although may have looked better on an old crt.

I already did it, i downloaded the wrong compiler in the CYGWIN, not the GCC-CORE.
I extract all the files and converted them into png, but the Project64 cannot load the textures, but other textures the plugin GlideN64 can load without problems.

I'm having the same issue with my n64 games with a pi3 as well

@mulder79
Hi did you get this to work in the end I have a similar problem with ipac 2

@jmac If you're on RPI3 recommended is a 2.5A power supply.

Hi, this is an old issue, but I just configured mine RetroPie few days ago.
I don't want overclock my device, this can means a risk for me. So, I was playing Tony Hawks Pro Skater, and I think the same issue was happening.
The solution for me was reduce the video quality (also the video clock) and skip the sound of music while playing (the music I needed to change on Game configuration trying to skip the Audio system calls).

As software developer I know some error happens on the game and emulator prints a lot's of messages behind the game. I think if I know the shell commend to make the N64 Retro Pie Emulator skip the log messages the game can run even better.
If anyone knows a command like this please tell me.

Thank you

tried setting up Xbox one controller and works fine thanks for the help mate!

Ah, that sorted it! Thanks for the reply. :)

In case anybody else runs into the same issue, setting mupen64plus_audio=0 in /opt/retropie/configs/all/autoconf.cfg seems to fix it.