For me the problem was that Device Index option was set to Disabled (Settings -> Input). Changing to XBOX One Controller (it’s the only controller connected to my PC) fixed the issue immediately.
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I’ve got a similar problem as yours，My ds4 controller is recognized by the retroarch at once,And it worked well。But i don’t know how after Several times of playing games，My ds4 Can’t navigate the retroarch,But it was successfully configured as port #0 and port#1
I use DS4Windows, emulating an XBOX controller. Using version 3.2.16 and everything works fine.