My recommendation regarding this would be to check the drivers available for the OS version you are currently using in your system.
Also, you could double check if the USB ports are enabled at BIOS level, the Intel® VBIOS has this option available, this could change for third party vendors.
Have you requested support from the manufacturer of your Motherboard? I understand this says Intel® but the full support is provided by them.
Firstly, understand that you only have 2 usb 2.0 ports. The rest are junk.
Next, you have a SATA/Molex powered USB 3 card installed on your PCIE slot as well. Hopefully you didn't do anything stupid and connect a usb cable from 2 to 3. Assuming you didn't do that, reset your BIOS to factory defaults. That USB3 card stomps all over your other resources from my experience. If the ports still don't detect, then run this:
Let it download everything. It's 12 GB so it'll take awhile. Update all your drivers. Reboot(which it'll tell you to do).
If that still doesn't work, then I would go lower level bug hunting and flash your USB 3 card (http://station-drivers.com/index.php?option=com_remository&Itemid=353&func=select&id=52&lang=en) and flash your motherboard bios to the latest(http://dlcdnet.asus.com/pub/ASUS/mb/socket775/P5Q-E/P5Q-E-ASUS-2101.zip). That's from 2009. You can see your usb 3 flash revision in device manager under usb 3 host controller/advanced.
If you're really desperate, you can use an updated(2012) modded bios here:
Which comes from here:
And lastly, check the capacitors on your motherboard. See if any of them are bulging or flowering. Your board is old enough to be approaching death. I don't know how well those boards are constructed, so I can't tell you what to expect. I wish you luck on your painful journey.
I am glad to hear you were able to get a fix for this from Microsoft directly.
If you require any further information or support, feel free to contact the Intel® Communities again.