Just experienced the same problem. Mine would play fine in PiFBA and MAME after XBOXDRV install but only “start” “select” and “A” (No Joy axis would respond) would work in other (retroarch) emulators. I Had to go back into and set retroarch controls again and it seems to be working fine now.
Not sure that it mattered but I did the retro arch controls through:
(Emulation station running) “Retropie” > “Retropie-setup” > “Set up” (Option 3) > “Configure input devices for retroarch” (Option 321)
followed typical retroarch super fast input mapping and did a re-boot.
Previously I had tried to do this straight from the option in the retropie menu off the emulator (“configure retroarch keyboard/joystick”) and it didn’t work.
[System: Retropie3/PI2/wired 360’s. Overclocked “Turbo” with PiFba, MAme4all, NES, SNES, SMS, SMD, MX, Vectrex, Atari 2600, 7800 totaling 7000+ roms on a 32gb card. Most MAME and PiFBA are working for the given romsets. (scraped about 30% so far)]
Still unresolved how to get the controllers working in MSX. Only working from keyboard now, but I’ve been to bust reconfiguring my MAME roms to 37b5 to research.