As it seems if you use the slots by 4x to 16x, bandwith isnt enough for pci slots but with 1x to 16x all worked
I`m having the same problem, with the same board GA-990FXA-UD5
I've got 6 GPUs connected (2x 280x, 1x 290, 2x 290x) using 1x to 16x unpowered risers everywhere, and only 5 GPUs are visible (using Windows 8.1).
Also I`m using 3 PSUs x 750W and since 4 cards work properly with 2x PSU (getting the maximum possible hash rate per card I suppose this isn't the problem).
Did I miss anything ?
EDIT: It seems the one from the 8x slot is not shown.