Has anyone sorted this? I have exact same issue and i am using clean install of B3 RC1 and lr-fba isnt picking up my joypad but other retroarch emus are fine.
Beta 3 did have some controller issues.
Try the RetroPie 3 final that is out now.
Sorry – just read you have RC1 – that should be ok, and works ok for me. Is it just the case that you cant add credits? Have you tried Rigth Shift?
RetroPie help guides: https://goo.gl/Yfy8kj