I suppose there could be something wrong with the internal USB header, but Jim is probably right.
I myself use an Asus bay device Amazon.com: Mb Accessory Front Panel USB 3.0 Box: Electronics
One thing to check: I have noticed that a new win 7 installation will often not install all the USB drivers
needed on newer motherboards. There will be little or no indication in the device manager about this. How I usually spot this is a lack of USB devices listed. My Asus board has 13 USB items listed in the device manager, under Universal Serial Bus Controllers. If you had say, only 8, that would be a sign.
This is remedied by running the MB installation disk, then updating as needed... perhaps a long shot but very easy to check.
My regular forums are down, so I thought I would pitch in here a bit