I've seen same issue. I doubt it is the port since mine self-resolves after a stopping and restarting of the ignition after the truck's control modules seem to reboot.
Mine occasionally exhibits exact same issue with center USB ports. It self-resolves after the truck is shut off and systems are allowed to reboot upon following startup. Happens probably 5% of time. Always comes back to life after a shutdown of the truck and restart. Annoying I know but not unexpected in vehicles that are 90% electronic.
Here is better video to audibly demonstrate the low freq rumble of my recently installed Flowmaster Super 50 Series Dual exhaust system.
The OEM Flapper was retained (similar to the Borla/GM) system. This is a 6.2.