@mitu Just wanted to say thanks for the help on this, it really means a lot. After losing some heart, I took another look over Christmas and the reset you suggested solved my joystick problem as well, so I've had a blast over the break playing on it.
Next stage is to go back into the retroarch.cfg and configure the second joystick when friends are around, and then it'll be good to go.
Thanks so much! And apols for not getting back sooner for your help :)