Bruh, same problem here on Windows 11. Autoprofiles ran fine when I opened RetroArch on its own, then stopped the second I launched anything through LaunchBox. Adding https://ds4-windows.io/ as a game under a new APPLICATIONS platform and starting it from BigBox brought them back. My RetroArch profile now loads on its own, F1 works on the pad again, and I stopped remapping keys before every session. Thanks for writing this up.