Hi Craig,
If you're not using a Z77 or Z87 chipset motherboard (or the derivatives of those chipsets), then your USB3 ports are provided via 3rd-party controller.
This opens the door to compatibility issues (similar to using a non TI chipset Firewire controller).
Also, if you have a keyboard connected to one of these USB3 ports, you may have noticed that you can't get into the BIOS when booting. That's because the USB3 port's driver hasn't (yet) been loaded. Once booted into Windows, the keyboard works fine.
One other thing to note:
If you have a USB HD connected to an Integrated (Intel) USB3 port when booting, it can change the boot order of the HDs... causing the machine not to boot into Windows (providing an error message).
As a rule of thumb, I'd recommend booting into Windows... then powering up any attached USB drives.
Many external USB3 docking-stations and enclosures automatically put the HD to sleep (if it's not addressed for several minutes). This can be a bit annoying... as it can cause delays (waiting for the HD to spin back up) when saving.