Bdtyktl

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.

Based on the symptoms you describe it sounds like your OS has USB 2.0 drivers but not USB 3.0 drivers.

I found a good summary of the choices for a similar 'XHCI Mode' BIOS setting in a post by tonymac user a6f691ac:

XHCI Mode = Disabled
- The on-board USB 3.0 port function like a 2.0
port

XHCI Mode = Enabled - The on-board USB 3.0 port function like a 3.0 port

XHCI Mode = Auto - The on-board USB 3.0 port function like a 2.0 port
before OS USB 3.0 driver load. If you reboot the OS, the on-board USB
3.0 port again function like a 2.0 port during this reboot BIOS phase before OS USB 3.0 driver load.

XHCI Mode = Smart Auto - The on-board USB 3.0 port function like a 2.0
port before OS USB 3.0 driver load. If you reboot the OS, during this
reboot BIOS phase, BIOS is "Smart" enough to avoid downgrade the USB
3.0 port back to 2.0 functionality before OS USB 3.0 driver load. So Smart Auto is faster than Auto on 2nd boot onward, but Enabled is
fastest once you are sure the OS has the USB 3.0 driver installed,
because it avoid the switching. Making the on-board USB 3.0 port
function like a 2.0 port is mainly to support OS installation or to
support OS that does not have build-in USB 3.0 driver, so that the USB
keyboard would still work if the user plug-in a USB keyboard or any
other USB devices into the USB 3.0 ports before the OS is installed
with the USB 3.0 driver come with the motherboard.

Background:

Each major version of USB has generally used a new different interface on the computer side, requiring different drivers (1.x: UHCI/OHCI, 2.x: EHCI: 3.x: XHCI). Newer interfaces work fine with older USB devices, so there is no reason to use anything but the latest on a fully up to date system. However, when you're installing an OS, even if there are available drivers for the OS for the latest USB standard hardware in the computer, you may run into a chicken-and-egg problem if the drivers aren't included in the OS install and the only way you have to install the OS and copy the drivers on is through a USB port. To get around this, systems either include dedicated older ports (for instance dedicated USB 2 ports on a system that also has USB 3 ports) or else some kind of a selection in the BIOS such as this one that lets you change ports to use the older interface standard on the computer side, and then once you've got the OS on and the updated USB driver installer copied to the system, change them back to get the best USB performance.

xHCI Pre-Boot Driver

Enabled The USB 3.0 ports are routed to the xHCI controller before booting to OS. (Default)

Disabled The USB 3.0 ports are routed to the EHCI controller before booting to OS.

When this item is set to Enabled, the xHCI Mode below will be automatically set to Smart Auto; when this item is set to Disabled, the xHCI Mode below will be automatically set to Auto.

source: http://mbforum.gigabyte.de/index.php?page=Thread&threadID=6484

On Dual-Boot between Windows 10 and Windows 7 (pro for both), the xHCI controller bypasses the legacy usb ports (loads no legacy usb ports). Setting xHCI to disabled allows the dual boot to function correctly under ASUS bios using EHCI controller.

The XHCI controller (Extensible Host Controller Interface) is the USB 3.0 controller. For all practical purposes, you can consider the terms synonymous. So, yes, it sounds like this will disable the controller and the associated ports entirely (unlike earlier controllers, the same stack handles USB1 and USB2 as well as USB3, so this is probably an all-or-nothing prospect).