I found this article and seem to have a similar Problem. Why is USB not working in Linux when it works in UEFI/BIOS?
MyConfig Fujitsu Board Qxx Chipset i5-2400
I use VPro KVM and the input doesn't work in debian jessie. Live CD and rescue mode are fine.
I tried an upgrade to Kernel 4.5.
To get network back to work I used
service restart network-manager in rescue mode.
Normal usb devices work again after replugging them.
I changed mainboard and CPU recently, but I had similar problems with the last system. I don't have a Gigabyte board. And tried nearly all settings in bios.
001:004 must be the vPro KVM.
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub Bus 001 Device 005: ID 046d:c529 Logitech, Inc. Logitech Keyboard + Mice Bus 001 Device 004: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
dmesg | grep '2-3'. The vPro KVM device.
[ 4.284230] usb 2-3: new high-speed USB device number 3 using ehci-pci [ 4.491046] usb 2-3: New USB device found, idVendor=8086, idProduct=002b [ 4.491051] usb 2-3: New USB device strings: Mfr=1, Product=2, SerialNumber=3 [ 4.491061] usb 2-3: Product: USBr Composite Device [ 4.491063] usb 2-3: Manufacturer: Intel [ 4.491065] usb 2-3: SerialNumber: 0001 [ 5.921587] usb 2-3: USB disconnect, device number 3
Why is it disconnecting?? In rescue mode it reconnects automatically. I can even launch lightdm from rescue mode and then use it with keyboard and mouse.
Other "real" USB devices have the same problem. The vPro device must be a virtual USB.