Just rebuilt my system with a new case and motherboard. My new motherboard (Gigabyte z68x-ud3h-b3) has two USB3 ports on the back which are not detecting the device plugged into them (currently my G510 keyboard) on a restart. If I plug in the keyboard while it's running there is no issue, it detects it fine, but if I restart it will power on the keyboard lights, but the keyboard will not be functional unless I unplug/plug it in again. I have the latest drivers from Gigabyte's website installed for the USB3 ports too. Any thoughts as to why these aren't working?
I have had this issue with a couple of other motherboards as well. It seems to be a limitation of the 3rd party controllers that are being used for USB 3. For your keyboard and mouse just use USB 2 ports and your problem should be alleviated.