Libretro with bluetooth gamepad

[dikdom]

Hi,
I have two generic (cheap) bluetooth gamepads and they are configured properly, as far as I see it: I can use both of them in ES to select an emulator/game and navigate the menus, I can use them in the C64 emulator (as two joysticks). The problem arises when I try to play with libretro games, like game&watch, snes games, psx, etc... The buttons of the gamepads are somehow mixed, and not recognized by the lr-XXXX emulator (while using a USB keyboard the games work as they should).
For snes I configured a different emulator (snes9x) and it uses its own gamepad controls: snes9x.cfg. It works properly.
I have the gamepad config files in /opt/retropie/configs/all/retroarch-joypads/ directory (Gamepad.cfg, "BT Gamepad.cfg"). Both of them contains the proper scancodes for the buttons, as far as I can tell, I checked with the jstest /dev/input/js{0,1} tool.
I have checked the /opt/retropie/configs/retroarch.cfg file and it has the magic
input_autodetect_enable = true
line, so all the libretro emulators should work according to the configuration. At least this is how I would expect.
Could someone tell me what configuration I'm still missing? Honestly, I didn't mess around with the core configuration files (except the c64 configs) so I would expect that it should work.
This is a pi3 config with the latest (1-2 week old) retropie. I have upgraded recently from 3.8.

Thanks!

[dikdom]

It seems that indeed, the configuration itself was the problem.
When I reconfigured the controls in the libretro GUI menu, it overwrote the /opt/retropie/configs/all/retroarch-joypads/xxxx.cfg files with some new values - different ones that jstest prints.
I had to edit the files for the special commands, like 'exit emulator', 'save', 'load', but basically it works now properly.
Interestingly the emualtionstation works as if nothing had been changed.
And nes, snes, psx games also understand now the key presses on my noname gamepads.
BTW: They are Terios T3, bluetooth stuff.