If they are rear ports, they are hard-wired into the MB. Not much you can do with that. But if they are front ports, the connector may have come loose, or is not making contact. Or that header is dead; try another.
If they are USB3.0 headers, try re-installing the driver.
I re-installed the drivers once and it didnt work, but I just did it again and for whatever reason they work now, so thanks i guess.