I don't know, I've never seen a USB3.0 cable like that. USB 3.0 is backwards compatable to 2.0 and 1.0-1.1. I would guess that the pigtail is for an extra USB 2.0 port.
Also make sure you have the cable pluged in right way, I had a bit of trouble with my Gigabyte 990FXA board, very easy to plug in backwards.
EDIT: on closer examation, it does look like that cable is in backwards.
MB's I own and in use:
ABit AV8
Gigabyte GA-880GA-UD3H
Gigabyte GA-990FXA-UD5
Asus Sabertooth 990FX