i found the problem for this mobo, if you are using 4x gpu with 4x to 16x, then you can add fifth one only by using the 1x pci with 1x to 16x, this way you can have 5gpu, if you want 6gpu, you have to use 1x to 16x on all of the pci slots, if you are using 4x to 16x, than you can only use four of the 5 16x pci slots.
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.