CheshAmoeba
Have you remap your controller under Emulstation?
When ES requests the "pad up" key, press the "DPadUp" key on the N64 controller.
When ES requests the "pad down" key, press the "DPadDown" key on the N64 controller.
When ES requests the "pad right" key, press the "DPadRight" key on the N64 controller.
When ES requests the "pad left" key, press the "DPadLeft" key on the N64 controller.
When ES requests the "joystick1up" key, press the "joystick 1 up" key on the N64 controller.
When ES requests the "joystick1left" key, press the "joystick1left" key on the N64 controller.
When ES requests the "joystick2up" key, press the "C Button Up" key on the N64 controller.
When ES requests the "joystick2left" key, press the "C Button Left" key on the N64 controller.
When ES requests the "a" key, press the "C Button R" key on the N64 controller.
When ES requests the "b" key, press the "A Button" key on the N64 controller.
When ES requests the "x" key, press the "C Button D" key on the N64 controller.
When ES requests the "y" key, press the "B Button" key on the N64 controller.
When ES requests the "start" key, press the "start Button" key on the N64 controller.
When ES requests the "Left trig" key, press the "L Trig" key on the N64 controller.
When ES requests the "Right trig" key, press the "R trig" key on the N64 controller.
When ES requests the "L2" key, press the "Z trig" key on the N64 controller.
In your mupen64plus.cfg, have you this configuration for the pad?
[Input-SDL-Control1]
version = 2
mode = 0
device = 0
name = "DragonRise Inc. Generic USB Joystick"
plugged = True
plugin = 2
mouse = False
MouseSensitivity = "2.00,2.00"
AnalogDeadzone = "4096,4096"
AnalogPeak = "32768,32768"
DPad R = "hat(0 Right)"
DPad L = "hat(0 Left)"
DPad D = "hat(0 Down)"
DPad U = "hat(0 Up)"
Start = "button(9)"
Z Trig = "button(7)"
B Button = "button(8)"
A Button = "button(6)"
C Button R = "button(1)"
C Button L = "button(3)"
C Button D = "button(2)"
C Button U = "button(0)"
R Trig = "button(5)"
L Trig = "button(4)"
Mempak switch = ""
Rumblepak switch = ""
X Axis = "axis(0-,0+)"
Y Axis = "axis(1-,1+)"
Rumblepak = ""