Mind sharing what board/Jetson module you've seen this on? I've seen this exact symptom very intermittently on a custom board and we've wondered for a long time if was an issue with a specific type of module (or manufacturing lot of modules).
My startup logic now power-cycles it until the PCI board is recognized; it works, but it's not a great solution.
echo 1 > /sys/bus/pci/rescan
sleep 1