Whats the card config, are the 480's in the 1, 3, and 5 slots, or the 1, 3, and 7 slots? I.e. is the Xonar in 7, or one of 5 or 6?
You can try moving the third 480 into a different slot (i.e. if its in 5, move it to 7), but I don't know what that would accomplish.
Have you tried putting any other PCIe cards in the slot you're putting the Xonar in (like a raid card or network card or something)? Maybe the slot is bad?
My only other guess is that because the board uses 2xNF200 chips to split 32 lanes into 64, the Xonar might be conflicting with something there. I'm just guessing here, but maybe the fact that the Xonar is "sharing" 16 lanes with one of the graphics cards might be confusing things, especially if the Xonar is running PCIe 1.1 signaling and not 2.0 like the 480.
Don't know, I was hoping you were running a 740G or something with limited lanes.