@atmosphere, in your commands.json file, make the ground field background instead of foreground. That way it will run in the context of the background service.
{
"trigger": "GPIO 6 on",
"command": "python /root/gpio6on.py",
"ground": "background",
"voice": "6 on"
},
Run this to install the background service:
/usr/share/triggercmdagent/app/src/installdaemon.sh