I figured out it was the rail from testing each GPU with it's closest rail. Then I found the GPU that didn't function in cgminer. So I tried it with a different rail and it started working. Hence I moved the power cable to another rail and got all five working. I could probably do six again by swapping out PSUs but the power consumption was going past the 1600W rating when I had six going. I had to underclock and turn intensity down to get it stable. If I were to do six again, I would use two 1000W PSUs.
To get six GPUs working, I used 13.1 on Windows 8 a 12.6 trick. I can't find the link at the moment but it's somewhere on this forum about six GPUs to work on a motherboard. Also no shorting PCIe slots on the MSI Z77 GD65.
I have the same PSU and Graphics cards as you and am struggling to get all six working. How did you figure out that one of your rails was malfunctioning? Also, did windows 8 see all six right off the bat? Just installed 13.1 and they worked?
I'm using an A4 FM2 processor with a gigabyte F2A85x-UP4 but so far its been nothing but a pain in the ass lol. If you have 6 msi r7950 twin frozr working good in windows 8 with that msi board, I might be making a return to amazon soon lol