I have the iBuffalo snes controller and I don't seem to be having any issues with the hotkeys. Although, I didn't try button 4 and 5. Perhaps my configs could help, it's mostly default though.

InputAutoCfg.ini ; 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 = R Trig = button(5) Start = button(7) Z Trig = button(4) C Button D = button(0) A Button = button(1) 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

retroarch-joypads input_device = "USB,2-axis 8-button gamepad " input_driver = "udev" input_r_btn = "5" input_save_state_btn = "5" input_start_btn = "7" input_exit_emulator_btn = "7" input_l_btn = "4" input_load_state_btn = "4" input_up_axis = "-1" input_a_btn = "0" input_b_btn = "1" input_reset_btn = "1" input_down_axis = "+1" input_right_axis = "+0" input_state_slot_increase_axis = "+0" input_x_btn = "2" input_menu_toggle_btn = "2" input_select_btn = "6" input_enable_hotkey_btn = "6" input_y_btn = "3" input_left_axis = "-0" input_state_slot_decrease_axis = "-0"

mupen64plus.cfg generated after game start

Joystick event string for stopping the emulator

Joy Mapping Stop = "J0B6/B7"

retroarch-joypads input_device = "USB,2-axis 8-button gamepad " input_driver = "udev" input_r_btn = "5" input_save_state_btn = "5" input_start_btn = "7" input_exit_emulator_btn = "0" input_l_btn = "4" input_load_state_btn = "4" input_up_axis = "-1" input_a_btn = "0" input_b_btn = "1" input_reset_btn = "1" input_down_axis = "+1" input_right_axis = "+0" input_state_slot_increase_axis = "+0" input_x_btn = "2" input_menu_toggle_btn = "2" input_select_btn = "6" input_enable_hotkey_btn = "6" input_y_btn = "3" input_left_axis = "-0" input_state_slot_decrease_axis = "-0"

mupen64plus.cfg generated after game start

Joystick event string for stopping the emulator

Joy Mapping Stop = "J0B6/B0"