@spudsmctoole And for your autostate thing, I've faced exact the same effect that the option was activated! .... I've written a small script that will alter your retroarch.cfg as you want.
You can find it here: Dirty Little RetroArch.cfg writer
You can call the script to disable autostate_save feature like this
$HOME/RetroPie/scripts/SetRetroArchCfg.sh "$1" "savestate_auto_save" "true" "false"