@dankcushions Thanks, resetting the configurations tools > emulation station seemed to help for emulation station, but as you explained that doesn't clear out any emulator-specific configs.
I know you said deleting .cfg files was a big no-no, but I deleted the rom name specific config files in the folders within
/home/pi/RetroPie/roms/mame-libreto/mame2003-plus
(but ONLY those named the same as the game ROMs)
EDIT: and now my arcade games that were going wonky are functioning correctly! NOW I need to get back to figuring out how to assign the spinner to tempest for example, without messing anything else up.