Need help with controller config please

So I set up my controller say for instance for the NES. I do the normal bind and have menu toggle to none, config per core, and then quit retro to save, But for some reason every time I launch a game if I push R1 it pulls up the xmb menu for retroarch and is not saving the config. Now this does this for all my units, NES, SNES, Genesis, etc… Am I missing something? Why is it keeping referring back to R1 for menu toggle? Even if I set it to toggle with a different button it keeps going back to R1. I just want to have the config save and load auto for like street fighter for instance so I can play, not push R1 to kick and then it shoots me into a menu.

I have setup controllers before on retroarch, but the process I use is slightly different.

I say that if you can, start with a clean retroarch.cfg file. That is, one that has not been saved after a controller configuration. If you do not have one, you can move the file you do have to another folder or delete it (though that might not be recommended if you have already setup a lot of other things like directory paths) because retroarch creates a new retroarch.cfg file if it cannot find one. Start up retroarch and go to settings > input > input user 1 binds > user 1 bind all and go through the process of configuring your controller. When you are done, scroll down to where it says “user 1 save autoconfig” and then quit retroarch. I think that “user 1 bind all” saves all your controller settings to the retroarch.cfg file while “user 1 save autoconfig” saves the controller settings to a seperate file in the autoconfig directory. Once you quit retroarch you can delete or move the retroarch.cfg file to another folder and start retroarch again. Because the autoconfig file was saved, it should recognize your controller anytime it is plugged in or paired through bluetooth.