Worst case scenario: your USB ports could be fried. You will need to buy either a PCI expansion card supporting multiple USB ports or a new new mainboard.
Less worst case scenario: the drivers for your USB ports are broken. Removing and re-installing your USB drivers would be the best solution. More often than not, USB 3.0 ports need specific drivers which are usually found on the installation media that comes with the mainboard. And if you misplaced the installation media, you likely can find these drivers on the manufacturers website as well.
Are you sure that the mainboard is supplied sufficient amounts of "juice"? All kinds of (very) vague and seemingly unrelated problems can occur when your power supply isn't capable anymore to deliver the +12, +5, -5 and GND required by your mainboard. You could try to use a different power supply and check if the errors still occur when connecting the USB keyboards again. A high quality power supply really makes a difference, but often people fit their PC with a cheap model power supply, so they can spend more on a (more) decent video card or SSD or whatever.
If you as builder of your own system can "save" a lot of money this way, guess where a manufacturer of pre-built consumer-grade PC's will spend as little as possible. And if these manufacturers move systems in bulk that really adds up.
Here in Paraguay you don't have much choice, but since I have been using Corsair power supplies (and the occasional OCZ) I spent much less time on workstation maintenance.