Is this one of those straight up USB3.0 controllers that does not also have a USB2.0 interface baked in?
You can tell in device manager, because there will only be a USB3 root hub, and no USB2 or USB1.2 root hubs.
If so, my guess is that this is a driver related issue with the USB host controller. (Microsoft and their insistence on their WHQL signed drivers, and forcibly updating drivers via windows update have a pretty strong track record of removing perfectly functioning OEM drivers and putting less than stellar, and even broken generic ones in their place. One of the many things I really dont like about windows 10.)
I will research it more to see if others have had this issue. I will presume for the moment that it is one of those usb3 only host controllers, which are almost always intel based. Give me a bit.
To help me find you a solution, (and because the friendly name is almost never useful), can you please put the PCI hardware ID for the USB host controller up here? you can easily get it into the clipboard from device manager. I can more definitively identify the controller, and hunt for known driver problems that way.
So far, initial digging suggests that there have been a number of people having problems with USB devices on windows 10, but most have been related to USB2 root hubs.