How to save config so it loads at next start? Reverts to default

Running on a Nexus 7 2013. Nightly build from three days ago.

Everything works just about perfect, SNES, NES, Genesis, the stuff I care about. Gamepad works too, a NES30. I can map everything, load up games, and enjoy. I set things up, save the config file, and go on my way.

But when I close the program and load it again later the emulator goes back to the default config file, retroarch.cfg. I know the one I used before is there because I can go into the menus and load it, but is there a way to make it so whatever the last saved config file made is the one that is used when Retroarch is started?

Dont save it, just close retroarch from rgui for make it save. Or rename you saved config file to Retroarch.cfg and replace with the old one.

Should that save the button mappings as well?

Yes, but that was somewhat broke on the 1.2 release. It is indeed fixed on the current nightlies

Updated to the latest nightly, so far it looks like the options are saving, will dig out my gamepad shortly and test that out too.