Ok firstly what device are you trying to connect to a USB port ? USB is only ever really intended to send / receive data at low voltages.
Some USB powered hard drives lately (high capacity ones usually) require a second USB connector.
Also not all USB headers / connectors can supply exactly the same voltage.
For anyone to help you please post some more info - ie device being used, if the USB socket is on the mobo or its via a case mounted socket or even a usb hub