@emrecaglar if you need any help to set it up please let me know - I went through some of problems with this combo (it's a bit more problematic than RetroPie for Pi :)).
For sure you can change priviliges for config files as you won't be able to save any config in RetroArch:
sudo chmod -R 777 /opt/retropie/configs/
Please just be mindful that this way you give access to this files and folders to EVERYONE which means that if someone connects to your computer then it has full access to all files and folders in this path.
In my case it does not matter as I don't have constant network access to this device (it sits in arcade cab with no lan/wifi) so not much of a deal for me :)
@Ecks The problem existed for a limited timeframe and it was an external factor at stake - not in RetroPie. The fact that you didn't experience it means you didn't run the installation at that particular time.
Actually I just saw the performance test...I think I will get a Pi4 and modify the Nespicase lol...I want to play ps1 dreamcast and some n64 Mame etc, the Pi1 B+ doesn't seems to be strong enough for all this.
No ideas from anyone? Disappointing... But I guess we can't expect to figure out a fix for everything. (especially if my friend is right)
EDIT: YEAH, my friend was right. Screen was dying. No longer functioning at all. Sorry to have wasted the time of anyone who read this - fix a dying screen with configuration changes is....kind of impossible.