Weird in-game joystick problem with n64 roms, used to work but not now.

[hobnobz]

Hi,

I'm running retropie-4.4-rpi2_rpi3 and for some reason with n64 games only, when I start the actual game play the joystick controls don't work. weird thing is like with 1080 snowboarding the selection part works but not the race itself. it's like it's using analogue settings just for that part. I can't work it out. I'm using a MicroTek Joystick setup.
I have poked around in the settings, cleared joystick and reset. same issue. I'm stumped. any ideas what this might be?

default emulator is been used: lr-mupen64plus
the InputAutoCfg.ini in the n64 folder looks like this:-

Microntek USB Joystick _START
[Microntek USB Joystick ]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
L Trig = button(5)
Start = button(11)
R Trig = button(8)
Z Trig = button(10)
C Button D = button(9)
A Button = button(3)
C Button U = button(6)
B Button = button(0)
X Axis = axis(0+, 0-)
Y Axis = axis(1+, 1-)
; Microntek USB Joystick _END

Thanks,
Hobnobz