I have a BIOS setting called XHCI Pre-Boot Mode. If I have this enabled USB devices which aren't plugged in at boot are never recognised, if I set it to Disabled then USB devices work normally. The brief BIOS description says "Enable this option if you need USB3.0 support in DOS." Which I don't, but it also says "Please note that XHCI controller will be disabled if you set this item as Disabled." So does that mean that USB3 is disabled with this option? Here's a picture of the screen:
UPDATE I subsequent BIOS update seems to have fixed this issue in that USB devices work even when not plugged in at boot with this option Enabled.