@mitu I have tried disabling it, it still doesn't work. I honestly don't know what the resolution is for my screen, I think it's 720x480. I'm actually using a car dvd player, the kind that straps onto the back of a headrest. I'm using the composite output.
EDIT: Ok then, I just rebooted without touching anything and it's working fine, so thank you for your help.
I think I found my issue. Apparently it make a difference as to which order you plug in the controllers to the USB hub - under normal conditions, I had the far left slot open, the second slot for my keyboard dongle and then the controllers plugged into the 2 ports on the far right.
When I was testing my new image, I had the bottom opened up and the unit was upside down. I plugged everything in the same as before, except in reverse (since it was upside down). As soon as I rearranged the plugs, all worked as usual.
@meleu thanks for responding, I've added my different controllers now, sorry for not doing this earlier. However I don't think this is of any importance since every controller (except for my bog standard keyboard) gives the same results.
@gautchh Attach and config a keyboard in ES, go into the emulator of your choice and enter the rgui menu. There you can navigate to Settings, Input and configure your controller. Make sure the right controller-device is selected and try bind all.
If your controllername does not show up increase the number of players (or devices) under Input and try again.
Another way to get your controller working properly is using xboxdrv, which emulates an xbox controller and makes mapping it in games easier.