Have you done this same thing with a "stock" RetroPie image before? You make it sound like it's something that works on RetroPie normally but not on your Freeplay Zero. That would be rather odd.
You said a couple differing things there, so I want to get this straight. Are you using WinSCP to try to transfer files and ALSO using PuTTY to SSH in?
If you SSH in, there are things that the "pi" user may not have access to. Offhand, I don't know if /opt/retropie/configs/all/autostart.sh is one of them, but I would guess that it is.
If you want to edit that file via SSH, you would need to do that as super user. Use a command something like this:
sudo nano /opt/retropie/configs/all/autostart.sh
You said a couple differing things there, so I want to get this straight. Are you using WinSCP to try to transfer files and ALSO using PuTTY to SSH in?
If you SSH in, there are things that the "pi" user may not have access to. Offhand, I don't know if /opt/retropie/configs/all/autostart.sh is one of them, but I would guess that it is.
If you want to edit that file via SSH, you would need to do that as super user. Use a command something like this:
sudo nano /opt/retropie/configs/all/autostart.sh
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Neo Geo Pocket Flash Cart and Linker Project ( http://www.flashmasta.com/ )
Avatar art thanks to Trev-Mun ( http://trevmun.deviantart.com/ )