I beleive that by installing the USB 3 controller you are taking PCIE lanes away from the cards, the same would happen if you had three GPU's running. Thats what im basing this on anyway. Your manual states that if 2 cards are used both in the blue slots then you get 16 x2 but if you add a third you get 16 x1 and 8 x2.
It would seem to me that its reading an aditional card even though its not a GPU and shutting the second card down to a x8 lane.
Pcie scaling tests have shown that its not too big of a deal anyway. I really wouldnt worry about it too much
Well, like matronix said, when you add a card to the 3rd PCI-e slot, it splits the 16 lanes of the second slot between them (so 8x/8x). However, it doesn't really matter as even the GTX280 doesn't bottleneck with an 8x PCI-e. I wouldn't worry about it because it really shouldn't affect your performance noticeably.