USB initialization is a part of the windows boot process so they should be up and running before there is any log-in window.
1) bad/wierd USB device? Unplug all usb devices except for the keyboard and mouse, or even try a different keyboard and mouse, and see if that solves the issue.
2) bad controller? try switching the keys and mouse to a different pair of USB ports. Each pair next to each other (left-right on a tower, top-bottom on a desktop) is on a different USB controller, so try them on a different pair.
3) lost drivers? Check your event log to see if it is re-installing the drivers for them every time you boot. Granted with an SSD the process would be nearly immediate (on my wife's SSD most items are ready to use before I can move my hand from the plug to the device).
4) Reset the BIOS/UEFI? have you tried doing a reset on the switch/jumper, and then go into UEFI and load the optimized settings? Is USB set to OS control in the UEFI?