We helped one of our clients fix a similar issue recently with their custom built AGX Orin carrier. Just like you they were also HW engineers, which I find to be a pleasant coincidence.
At the end, we found the issue was the pinmux and device tree configuration. That being said, I don’t think that could be the case in your specific station, since that same pinmux and DTB you are flashing to your Devkit SOM via your custom carrie board and is working as expected.
I would lean towards thinking that there is something that is already flashed in devkit SOM and not flash on your stand alone module, that for some reason the flashing procedure is failing to flash. And that is causing USB issues.
I see in the last image you sent, the very last message recommends checking the systemctl status of a service. Can you try running that command and sharing its output ?
best regards,
Andrew
Embedded Software Engineer at ProventusNova