Amiberry is an application, not an SD image to itself. When I flashed the SD card, it was to burn the latest version of Raspbian
I believe I might now know what the problem is or at least have reached the point where I'm able to peak over the wall and get a glimpse of what might be happening.
I spent much of last night looking for references to usb enumeration failures linked to the RPi, when I discovered this thread https://github.com/raspberrypi/linux/issues/273
admittedly it is a little deprecated by now, but it did get me looking at my usb port speeds.
Directly connected to the pi, the joypad will not function, however hook it up to a two port hub that is linked to the pi and works fine. I dont believe this is a hardware fault, as I was duplicating all my actions on a spare 2B+, which behaves exactly the same as the Rpi 3b. Also it is worth noting this joypad works fine in my Ubuntu Laptop. So I'm confident we aren't looking at a bad cable.
My only guess is that something has changed between wheezy and stretch when it comes to handling low speed devices or there is a bug.
I can't offer anyone a solution and I would welcome a more educated opinion from anyone more savvy with Linux.
If anyone stumbles across this thread and we dont solve it later on, I suggest you try out this following command in your config.txt
This slows down your usb ports and might eliminate enumeration errors.
Blackadder: Right Baldrick, let's try again, shall we? This is called adding. If I have two beans, and then I add two more, what do I have?
Baldrick: Some beans