had this a couple times a while back.
fixed it by deleting everything related to retroarch and copying it all back from the original nightly zip.
not sure why it happens
after comparing my retroarch folder with a fresh downloaded one, i finally managed to fix it by removing the .cfg file in the 'autoconfig' folder.
but when i began to reconfigure my stuff again, i ran into a new issue. before, i set right stick click as the menu toggle button and i could click it to enter the menu and click it again to go back to gameplay.
but for some reason, going back just didn't work anymore, so that i had to navigate back all the way to quick menu and resume every time... so i reverted back to the backed up config and left it be..