Upon inspecting the 5.1.5640 package we spotted some interesting driver files in the $WinPE$ folder which looked very much like USB controller drivers. At that point we booted up the OS X side of the dual boot and enabled NTFS write support on the Windows drive.
We then replaced the old version of the Boot Camp support files (make sure you extract all folders from the ZIP file or the installer will moan) then copied the suspected USB3 drivers to C:Windowsinf which meant if the files were correct they’d get automatically installed by Windows as sysprep completes. We also placed the contents of HCSwitch into the inf folder as well just to be sure.