Hi fhardy,
What’s the Jetpack version in use?
Let me check GPIO04 in your case.
It seems you’ve configured it as following:
Please confirmed the generated pinmux/gpio dtsi have both been placed to correct directory and you’ve also specified PINMUX_CONFIG in board config.
To control this pin through gpiod, please run the following command.
$ sudo su
# gpioset --mode=wait `gpiofind "PCC.01"`=0
# gpioset --mode=wait `gpiofind "PCC.01"`=1