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jiggawattI noticed this issue as well, and I think it has to do with a recent commit/change to the setup script. It’s failing to find the sixpair program. You can accomplish what the setup menu now seems to fail at by manually executing the sixpair program
/opt/retropie/supplementary/ps3controller/sixpair
That will register your PS3 controller to the BT dongle on your Pi. You’ll need to restart (stop/start) the sixad service on your Pi once that’s done. Make sure hciconfig shows “UP RUNNING PSCAN”
Then press the PS button and after a second or two it should register.
Hope that helps.