It sounds like a lot her board issue, kind of. The card is obviously working if you switched them, removed other variables and can get it to work.

Make sure your driver's for your chipset and motherboard are fully updated, check on the Asus website for anything that may be out of date. Also, try an older driver instead of the newest one.

You are only showing more and more that it is probably a operating system/motherboard driver issue. If the gpu bios didn't help, it isn't a gpu bios issue.

Did you check your motherboard drivers, and device manager list? With the quick answer, it seems like you haven't yet. Since there are many people using 980's with the x99 deluxe, then it is pointing that something else is wrong, especially since nothing changes when you make changes to everything else.

It could be a faulty psu for sure. If the voltage is dropping enough to cause an issue and then recovering, that could be part of it.

Did you check to verify that the drivers are fully up to date for things like the chipset? Just glancing in the device manager doesn't show the newest driver, it just shows that there are drivers, even if they are out of date.

Next, try down clocking your gpu. Take it down - 100 Mhz and see if the problem persists. I doubt it helps, but it may provide more stability.

How many cards do you have? 2 or 3?

Did make sure that the dip switch under the Asus chipset heatsink that is used for 2way or 3 way sli configuration is in the correct position?

Not using modified GPU drivers, WHQL 350.12.  I have tried both my old AX1200 (which is what I used when I first built the system) and now I am running an EVGA Supernova 1300, but no noticeable difference.  I have checked the PCI-E power cords with a PSU tester and it has a solid voltage on all of them.  
 
If I let the system boot with the basic display driver and then re-install a clean 350.12 it still shows that one card as a basic display driver.  The other 2 cards show being 980s in the device manager.  The primary card in device manager's status says "This device is not working properly because Windows cannot load the drivers required for this device. (Code 31) The driver trying to start is not the same as the driver for the POSTed display adapter."
 
I have downloaded and re-installed the x99 Chipset driver (v10.0.20) and MEI driver (V10.0.0.1204, and windows update will update this version too) from ASUS's download page and re-installing seems to have no effect either.  
 
I am running 3x980s and yes the switch on the motherboard is set to 3-way SLi and the white indicator LEDs are next to where I have the cards installed.
 
When I first started having this issue when I first built the system, it simply wouldn't initialize the primary PCI-E card at all, not even showing the BIOS (red LED next to the primary PCI-E slot stayed lit), but the system would fully boot and I could connect with Teamviewer.  It at least starts with some sort of video now, but doesn't initialize the driver.
 
Any further ideas?

Sajin
Have you tried completely wiping your GPU drivers using DDU then reinstalling clean with the latest video driver? Try a older driver too if you haven't already.

I will give it a shot right now.

Well after one of the BIOS updates it stopped showing the red LED.  Now it will at least initialize.  I was pretty sure it was a motherboard issue myself too, but the troubling part is that it works sometimes and if I never shut down the PC it runs solid.  Sure enough though if I restart it the same issue comes back.
 
When I was first having the problem after my initial build I was switching the cards between all the slots, but it only happens to whatever card is in the primary PCIE slot.  
 
It's not super fun moving them around anymore because they are all watercooled with SLi link pipes between them.  Not so easy to just pop them out and move them around.  I was hoping after I got the board that other people were having the issue, primarily the device manager showing "The driver trying to start is not the same as the driver for the POSTed display adapter." but it doesn't seem like a common x99 issue, or even an ASUS X99-Deluxe issue.
 
I uninstalled the drivers with DDU in safe mode, and when installing them again after windows booted I had the system freeze like this (picture attached).  First time I ever had the system freeze like that.  Restarted and clean installed the drivers again but I still have it showing the Microsoft Basic Display Adapter.
 
Motherboard issue most likely, correct?  That was my gut feeling, but I have never seen/heard of this problem before doing all the years I have been doing computer repair.
 
https://www.dropbox.com/s...zKtsCxd6CLAXOWONHRKMMa

Does you board not have a molex connector to supply addition power to the PCI lanes?

I didn't think so, after staring at pictures of the board. I do like the look of that board.

rgspro
Yeah it's an excellent looking board that is for sure.  Here is what I have configured...
 
It started doing it again, so I am going to up the system agent voltage to 0.3 offset.
 
https://www.dropbox.com/s...dGhLblivlMAuTM5Eg4WQaa

Nice Rig you have, If you use https://www.flickr.com you can display your images.
Dropbox does not allow it.
 

rgspro
Pushed the CPU Core to +.30v and still having the same issue.  I wish I found some consistency after changing some settings.  Hope the PCIE slot isn't bad.

If you set your Bios to all the Default Settings do you still have issues?

Is it possible that having 2 USB powered HDDs plugged in would cause any power issues?  Is it possible to draw too much power on the boards USB ports to cause other hardware issues?

I dont think that would necessarily work because the issue doesn't happen until you get into windows.  I know some of the other ASUS boards let you disable a PCI-E slot, but i dont think this one does as far as I can tell.  
 
I could try taking out one of the cards, but it would be a bit of a procedure with the watercooling and all.  The board supports 3 way sli, so i technically shouldn't have to take it out.  Just getting frustrating that every time I start the system there is this issue that takes 10-15 minutes so sort out every time I have to reboot it.

Sounds like a PSU issue.

It's not a PSU issue because I have a PSU tester and all the PCIE cables test fine as well as the MB cable.  Besides, I have already replaced the AX1200 I was using with an EVGA Supernova 1300.
 
Talking with ASUS phone support for 10 minutes and they decided to recommend an RMA.  It was pretty lame that their email support said "are your video cards on the approved hardware list?"  What a load of crap that line was.
 
Phone support was much more efficient rather than waiting 2 days for email replies.

I got the motherboard replacement and it seems a lot more stable.
 
I do note now that when I do normal restart after changing any of my overclock settings in the bios once it gets to windows it will be on the Windows Basic Display Driver on the first card. Letting the system restart itself after saving the bios will give me this problem almost 90% of the time. If I power the system off and do a cold boot I no longer get the issue.  Is there some weird CPU/DRAM setting that I can change to get it to restart normally?  Is 4.4 just a bit too ambitious for a 3-way 980 GTX sli system on the X99-Deluxe?
 
I'm getting 4.4GHz at 1.29v (1.28v will get BSOD on stress) with my ram at 3017mhz at 1.35v. (125.7 x 35) Does that seem pretty average? The whole system is on that dual 480 rad/pump custom loop.