Buttons not working - USB works

[Flavor]

That’s interesting. It seems like the joystick is working, as you said, in jstest.

In EmulationStation, if you have a usb keyboard plugged in, you can hit Start (maybe space bar?) at the main menu. Then select Configure Input. Then on the Freeplay hold A when it asks.

There’s another way to delete the current config and have it ask to config the inputs at bootup, but I don’t recall offhand. I’m just out on my phone right now.

Thx for the information. I can configure the input but EmulationStation only reconize the usb keyboard...how is this possible?

I really don't know. I'm pretty confused about it, now. If you could image the SD card and somehow share the file with me, I can try to investigate. I don't even know what next step to take for the remote diagnosis.

I just checked, and here's where the joystick configs are stored.
in the /opt/retropie/configs/all/retroarch/autoconfig directory
and in /opt/retropie/configs/all/emulationstation/es_input.cfg

Maybe show the output of
ls -la /opt/retropie/configs/all/retroarch/autoconfig
cat /opt/retropie/configs/all/emulationstation/es_input.cfg

You could also do this:
cd /opt/retropie/configs/all/retroarch/autoconfig
rm *
rm /opt/retropie/configs/all/emulationstation/es_input.cfg

Then, after you reboot, at the next bootup it should start up and go directly into the joystick input. I think that's probably worth a try, but it could mess other joystick/keyboard configurations that you might have. Who knows, those could be what's messing things up here, too???