Any poor quality connector can affect a sector scan and drive performance. Doesn’t matter if it’s connected to a corroded usb port or a bent internal sata, at the end of the day if you’re getting disk errors it’s best to measure using two methodologies/data pathways.
Just a thought, and it seems less applicable to your situation given the software experience you’ve described, but I’ve had this happen to me with a faulty display cable. Have you tried a spare one?