Retroarch-joyconfig keeps mapping wrong keys

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Hey guys I managed to get my 360 wireless controller going with this guide https://github.com/retropie/RetroPie-Setup/wiki/Setting-up-the-XBox360-controller this guide and everything was working perfect, I managed to play the first level of Super Mario Bros but then found the blinking light in the middle of controller to annoying so I looked around for a way to get it to stop blinking. https://www.petrockblock.com/forums/topic/remove-xpad-and-use-xboxdrv-instead-to-stop-controller-light-flashing-constantly/ This is what I did, blacklist xpad and repeat the steps in the first guide. Now however a strange thing is happening when I tried to configure the controller with ./retroarch-joyconfig -o /opt/retropie/configs/all/p1.cfg -p 1 -j 0. The button I press are not the buttons the Pi thinks I pressed, for example the select/start buttons are supposed to be 12 and 13 but the PI insists I press 8 and 9. When I run jstest /dev/input/js0 it shows the correct buttons being pressed but not during ./retroarch-joyconfig . I tried to manually remove the wrong mapping in retroarch.cfg and replace it with a button configuration found in Advanced Configuration at wiki but it did nothing. The weird configuration is still in effect even though I deleted It from retroarch.cfg
Advanced Configuration I got from wiki:
i`nput_player1_joypad_index = 0
input_player1_b_btn = 6
input_player1_a_btn = 4
input_player1_y_btn = 7
input_player1_x_btn = 5
input_player1_l_btn = 10
input_player1_r_btn = 11
input_player1_start_btn = 13
input_player1_select_btn = 12
input_player1_up_btn = 0
input_player1_down_btn = 1
input_player1_left_btn = 2
input_player1_right_btn = 3
input_exit_emulator_btn = 15
input_menu_toggle_btn = 16`

[paulb]

Hi,
I am a newbie, but have you check snes9x.cfg in pisnes folder ?
Settings in this cfg overrun retroarch .cfg.

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