You didn't say what OS you were using. Assume 10? While this could be related to BIOS rev... more likely its microsoft's USB driver in the OS. Removing all USB connections from the boards headers was a good troubleshooting step.
Is the nirsoft program the only app telling you USB is operating at a reduced speed? Does the OS report this?
What's happens if you disconnect/reconnect a device after resume from sleep? Does it then operate at full speed. I'd recommend performing your own tests to verify connection speed and bandwidth, and not rely on software, which I don't believe does benchmarking. Or does it?