I've been setting up a new water cooled system using an SR-2 board over the past week or so, and everything went well except for this problem, and i've tested several possibilities and still no joy....Here's the list:
 
1: I swapped that video card that wasn't working on PCI-e slot number 5, with one that was working on PCI-e slot number 3, and the same thing happens...The card when installed on slot number 5 still doesn't work,even though the card itself is good, as it works on slot number  3.
 
2: I swapped the PCI-e power connectors between those 2 cards to make sure it isn't a bad rail on the PSU...It's not that either as the same card still doesn't work on that particular slot.
 
3: All the cards are firmly seated in their slots and i moved  the jumpers on the motherboard for PCI-e slots number 2,4 and 6 and disabled them....That third GTX580 still doesn't show up.
 
4: Tried a different SLI bridge that came with a previous motherboard i used to run....Still no joy.
 
5: Flashed the motherboard to the latest BIOS available...Still the same thing, only 2 GTX580's are detected in windows device manager
 
6: I moved all 3 cards to PCI-e slot 3, 5 and 7 and at that point, only 1 card was visible in device manager( only the card on slot number 3 was the only one working), so there might be a problem with PCI-e slot number 7 too!!!...
For those wondering, i use a triple screen setup and know wich card is connected to what display....
 
The only thing i can think of to try next is connecting that additional 6 pin power cable from the PSU to the connector right beside the first PCI-e slot, because other than that, i'm running out of ideas here.....Could there be some setting in the BIOS that relates to the PCI-e card detection perhaps?
 
 

Yes, please use the 6 pin connector for the PCIe slots and test again.

No difference at all.....I enabled slow boot in the Bios and removed the classified logo option and the board just detects 2 cards, not all 3 of them...

Where are the leds located?
 
As far as the jumpers go,i only have them disabled for slots number 2,4 and 6, wich are blocked by the stock coolers on the video cards anyhow, but i had them all enabled previously and it was the same problem....Only 2 cards are detected.

27 is the cpu temperature. Right under where the notch is on the PCIe slot there should be a small red LED.

27 is the cpu temperature. Right under where the notch is on the PCIe slot there should be a small red LED.

 
Would that be on the end where the locking mechanism is located?, or the end that provides power for the slot itself..... It's hard to see anything with a double wide air cooler on each card.

Couldn't see those even if i wanted too, since the air coolers completely block that area anyhow...
 
But all 3 work now and it was because of my fault, as i plugged in that extra 6 pin cable i tried earlier not in the additional PCI-e connector, but on the auxiliary power connector when going for heavy duty overclocks on CPU 1....The connectors are right next to eachother and they're identical....DOH.
 
Homer simpson moment...

As long as its up and running everything is all good.

Nice rig you got there
Which CPU's do you have and what type of mem.
Do you have enough radiator power with just one 360 or is it a 420?

I've got another SR-2 laying here that I want to get some CPU's for, does the X5650's support x10 mem?
 
I believe a single 360 should be enough if you don't plan to OC to high and crunch 24/7. I'm using one 420 and a 360 on my CPU/MB loop and a 360 on the GPU loop but I'm folding/crunching 24/7 using X5690's at 4,5 GHz. Didn't have room for the rads inside the case so I made a stand for them outside instead.

Not too bad considering that one radiator is handling everything:
 

 
Averages about 55~60*C and that's only on the second CPU After the water has already passed thru the first, while the TJ when the CPU starts to throttle down is 95*C, so i got a decent amount of wiggle room to try out some O/C.....

I'd have to run it again but i'm still in the middle of installing a lot of updates, though i am thinking about unplugging the PWM wire for the pump, as it's programed to go to full speed when it's not connected and see where the temperatures end up..
 
I think the cooling can do better still, but i'll do it when all the other stuff is installed and configured.....