I am having very similar issues with a Gigabyte 990 UD3.
With 3 cards directly to the 3 16x slots it works fine.
With 5 cards all plugged into 1x risers, only 4 cards get detected in Windows. That is with none of the slots shorted.
The card that isn't getting detected is the card plugged into second (middle) x16 slot. Both of the others and both of the 1x slot cards get detected and mine OK.
If I short the presence mod on the 1x slots it makes no difference.
If I short any of the x16 slots with the presence mod, the motherboard WILL NOT power on at all. As soon as I pull out the shorting wire, it powers on.
I will start a separate thread here with its own bounty:
https://bitcointalk.org/index.php?topic=387663.new#new