Hello, I have stumbled across another issue!
I changed the Input settings (changed some hot-keys and ABXY keys), and then I did all the normal stuff:
Save Auto-Config -> Back to the Main Menu -> Save Config (saved as retroarch.conf)
All was good until I turned off the Live machine… when I booted it again, poof the changes were gone! D: It has already happened 2 times to me, its very frustrating to do it again >:(
I think its a bug in live mode, the input settings are not being stored 
Or did I mess up something? Hope someone can help me, Thanks in Advance 
P.S I am using the PC Edition lakka btw.