@Zing thanks Zing. It was user error.
I've remapped the controls in the autocfg file.
I've removed the n64.flatfolder and replaced with n64.configfile=dummy.
When I load a Rom no controls work. I'm running the libretro mupen64plus emulator if that matters?
The autocfg file still has the changes after reboot and if i put the flatfolder line back in the changes dont take effect. What am i missing?