Hello wvcadle, thank you for sharing your question in Intel Communities.
In Windows* 8.1 the USB 3.0 driver is already included with the operating system. Just in case, make sure you have all Windows* Updates installed.
I recommend checking with another USB 3.0 if possible, just to see if the same issue occurs; that way you can narrow the cause of the issue to a single device.
You may also contact the system manufacturer for further assistance, you may verify with them if there is an option in BIOS to allow those ports to function as USB 2.0 or 3.0, similar as the one described here.