Missing USB 3.0 Header Pin

So I swapped my system into my new Air 540 case from my old Carbide 600t. I never was able to use the front USB on the 600t as it didn't plug into the motherboard header, instead it was a cable that plugged into a back io usb port, so I decided not to bother with it. Anyways, when swapping out the motherboard into the 540, I noticed a pin on the header was missing. Is the missing pin absolutely necessary to function? It appears to work and seems to be hitting faster speeds than the back i/o ones. The back i/os cap out at about 170 and the front is hitting 200-210. I circled the missing pin in the image bellow. 


The ID pin is used for USB OTG and should not cause a problem with most devices.

I believe the missing pin is so that you don't plug in the connector the wrong way.  It should be on USB 2 and HD Audio headers as well.

Okay, I have two missing pins. I was referring to the ID pin, the one I circled.