In my case, it was because I registered the PS3 dualshok controls, using the xbox360 driver ... In emulationstation it works ... But in RetroArch it does not. The solution was: uninstall the xbox360 driver and re-activate the ps3 dualshock official driver, when rebooting ... Resigne the buttons in emulationstation, I recognized as ps3 dualshock command and I work the retroarch controls in all the emulators.

There is a new input mapping screen starting with RetroArch 1.7.2 - https://forums.libretro.com/t/new-input-remapping-menu/15584 - and as a consequence the previous re-mapping files are not working. I think that's what you're experiencing. Can you give more details about your system - as requested in https://retropie.org.uk/forum/topic/3/read-this-first ?

Glad to hear that! I find your hardware setup very clear and logical. So far, I did not find anything on the driver site. You mean it was an issue with a configuration file of RetroArch, right?

@phantomthrill What's the RetroArch version you're speaking of ? What's the problem you were having ? RetroArch uses the A and B buttons to navigate in the RGUI - that's the default and it matches the Emulationstation way of navigation/selection.

@hank-scorpio How do you have the controls attached to your Pi, are they connected directly to the gpio or is there a usb interface of some description? Also, you should check out the read this first link at the top of the forum pages (https://retropie.org.uk/forum/topic/3/read-this-first) and complete the information requested in there in your post.

@w44dde your issue is pretty common, check your wires on the joystick. I bet you have the wires connected "upside down" on one of the joysticks. Simple fix should be just to switch the wires connected to the joystick for player 2.