When I enabled Hyper-V (virtual machine support) on my desktop PC my USB devices wouldn't work at bootup. When I remote connected into the PC and went to the device manager I noticed that the USB Host Controllers had failed to start. Disabling and re-enabling them made them work, but once I rebooted the problem persisted so I went digging through my UEFI BIOS. From here I had options for USB Legacy Support and USB EHCI Hand-off. USB Legacy Support was enabled while EHCI Hand-off was disabled. Apparently this does not work well with Hyper-V. Once I changed EHCI Hand-off to enabled my USB devices started to work with Hyper-V enabled.
So, if you're having trouble with your USB devices such as mouse and keyboard not working with Hyper-V Enabled, dig around in your UEFI / BIOS menu for USB options such as EHCI Hand-off.