Problem with config files and Threaded Video setting

I realize this might not be the correct place to get help about this issue but it does involve Retroarch so hopefully someone might have the answer.

So I recently bought an Arcade1up Marvel Super Heroes Countercade and since it can be soft modded to run Retroarch/Batocera, I figured I should try that. And sure enough, it works fairly well and it will suffice for my purposes. However, the hardware inside the mini cabinet is limited so to run some games properly I have to activate the Threaded Video option. I’ve read that threaded video is supposedly something that should be avoided but it is the only solution I’ve found that fixes the issue, that being a horrible audio stuttering in some games.

The problem I’m having is that I can’t make the option stick, every time I restart a game were I have previously activated threaded video, it is deactivated and I have to do it again. I’ve looked through the config files, and I’ve determined that both the game .cfg and retroarch.cfg have threaded video listed as ‘true’ but a third file, retroarchcustom.cfg still lists it as ‘false’. If I try to manually change it to true and save the config file, the next time I start up the cabinet, the option is switched back to false in the file. I’ve even tried deleting the entire file, but it’s restored exactly as it was upon next boot.

I don’t know if retroarchcustom.cfg is the true culprit but whatever the case may be, if someone can at least direct me to some kind of solution so I don’t have to reactive threaded manually video every time I start a game, I would be grateful.