I have find the solution. in my case i’m using for neo geo emulation gngeo version 0.7. Seems that gngeo don’t use the same joystick configration file as the other emulators in retropie (retroarch.cfg).
gngeo looks for the joystick configuration on the file gngeorc that it’s ubicated in /home/pi/.gngeo/ so for change the joystick configuration file for neo geo roms this file should be edited and modify the line p1joy to fit our controller schema.
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