PS3 Controller & N64 - Controller not detected.

[razinx]

Pi Model or other hardware: (Pi 3B)
Power Supply used: (2.5A)
RetroPie Version Used (4.1.3):
Built From: (Pre made SD Image + personal mods)
USB Devices connected: KB
Controller used: PS3 (via Bluetooth), Xbox One USB, Clone PS3 USB
Error messages received:
Log found in /dev/shm/runcommand.log (if relevant):
Emulator: mupen64plus

Looking for some assistance please.

I have RetroPie 4.1.3 up and running almost perfectly, except for N64 and controls.

If using the default emulator, Mupen64plus-GLide64 the roms run, but my PS3 controller is not detected, or least no buttons work...

If I use lr-mupen64plus then everything works, accept this emulator tends to have poorer performance, so ideally I'd like to use the non lr emulator.

This had worked initially, but for some unknown reasons to me it stopped working with any controller (had worked with an xbox one controller, but that also no longer works either).

This is my InputAutoCfg.ini, which does see the PS3 controller,

; Keyboard_START
[Keyboard]
plugged = True
plugin = 2
mouse = False
DPad R = key(100)
DPad L = key(97)
DPad D = key(115)
DPad U = key(119)
Start = key(13)
Z Trig = key(122)
B Button = key(306)
A Button = key(304)
C Button R = key(108)
C Button L = key(106)
C Button D = key(107)
C Button U = key(105)
R Trig = key(99)
L Trig = key(120)
Mempak switch = key(44)
Rumblepak switch = key(46)
X Axis = key(276,275)
Y Axis = key(273,274)
; Keyboard_END

; USB,2-axis 8-button gamepad _START
[USB,2-axis 8-button gamepad ]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
Z Trig = button(4)
Start = button(7)
C Button D = button(0)
A Button = button(1)
R Trig = button(5)
C Button U = button(2)
B Button = button(3)
X Axis = axis(0-, 0+)
Y Axis = axis(1-, 1+)
; USB,2-axis 8-button gamepad _END

; Sony PLAYSTATION(R)3 Controller_START
[Sony PLAYSTATION(R)3 Controller]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch = button(1)
Rumblepak switch = button(2)
C Button D = button(13) axis(3+)
C Button L = axis(2-)
Z Trig = button(10)
Start = button(3)
Y Axis = axis(1-,1+)
DPad U = button(4)
C Button U = button(15) axis(3-)
A Button = button(14)
DPad D = button(6)
X Axis = axis(0-,0+)
R Trig = button(11)
DPad R = button(5)
B Button = button(12)
DPad L = button(7)
C Button R = axis(2+)
L Trig = button(8)
; Sony PLAYSTATION(R)3 Controller_END

I will note the keyboard does work, but the xbox controller is no longer present in the list, while PS3 is, but doesn't work. I'm guessing the USB, 2 axis 8 button gamepad is probably my clone PS3 controller (also does not work anymore)

I removed the mupen emulator and redownloaded it from source, but no change. Hoping someone can shed some light one this one, as this is the only thing stopping me from having a perfect setup.

Thanks!