My new Shuttle had a similar problem. There was a BIOS setting under integrated peripherals. You could set USB1.1 only, USB 1.1 + 2.0 or 2.0 only. I had mistakenly left it at 1.1 only, once I changed it and restarted the box Linux suddenly discovered some ehci devices that weren't enabled before. So I'd certainly look in the BIOS