some case manufacturers dont even used keyed plugs - they have 8 independent terminals.... so it is VERY easy to screw it up.
Sometimes, they are plugged into the connector that is also used for the external soldered ports. Make sure your motherboard has specific USB ports... if you have different ones, try them.
Also, doublecheck that BIOS.... mine can enable, 2, 4, or 6 ports. Forget about device manager or drivers.