Thank you! that was the problem The SD card was full like 100% full!. I free-ed up some space and my favourites etc, are being saved. I tested restarting emulation station and re-booting the Pie. All working fine now.
I feel like a fool! Thank you for your help.
Not a complaint, but a request: it might be nice to get a big fat warning if settings cannot be saved due to no SD card space. But from now on I will make sure to leave some space on the SD card.
@jonnykesh have you ever heard of the controller connecting via Bluetooth, retropie detecting the game pad, but NONE of the buttons working on gamepad?? I’m going to try another gamepad, this is most recent 1.23 firmware update with the new-ish SN30 Pro.