OK so I got a cheapo HDMI capture dongle and was testing it with the A600GS... worked fine even got audio through HDMI

(for a while!!)
I was trying the games I installed during Saturdays YAG meet (
https://youtu.be/AzPBu7f71zc ) and the USB joypad didn't work on any of them, works fine on the menu system just not in game... when I was installing the games I did have a Zipstik and a CD32 joypad in the 2 9pin ports and I was switching which was active as port 1 depending on whether I was installing a CD32 game or not... all games worked fine on the day using the 9pin controllers.
Games I installed before the YAG meet work with the USB joypad.
I installed the latest update just before packing up the machine to take to the meet.
So I thought I'd test if they still work with a 9pin joystick set as port 1... and I can't get the 9pin ports to work again... I have footage this time... OBS screen capture with a p!ssed off looking old bloke on webcam in the corner of the video furiously pressing buttons

Uninstalling the game and re-installing gets the USB controller to work in game.