Manually set your pci-e lanes to GEN3 mode instead of AUTO. See if that fixes the black screen issue.

Same thing on GEN3...
 
If I enable Compatibility Support Module (CSM) the 1080's legacy BIOS loads and I can see and access the UEFI BIOS settings of my motherboard. Same thing on the slave BIOS..
 
Again here's what I see: I press the power button, PC boots, the motherboard beeps and the red VGA_LED error thingy on the motherboard stays lit all the time. When windows loads it loads the display driver then I can see the Windows lock/login screen (VGA_LED stays lit all the time). This means that I cannot access advanced startup settings, safe mode, the motherboard's UEFI BIOS Settings with the card plugged in unless I turn on CSM so that the 1080 loads the legacy BIOS.
I have the most up to date BIOS for my motherboard (Asus Z-97-A), and when i pull the 1080 out and place the evga 970SC in its place, I do not see any of these issues.
 
 
I thought it could be a BIOS issue in the 1080, but from my understanding it has two BIOS chips, and both are doing the same thing.
 
Please give me more troubleshooting tips/suggestions.
 
Update1: I unplugged the display cable, did a power cycle for the system, and now it doesn't POST with the 1080 installed..
Update2: I unplugged the CMOS Battery and the Motherboard BIOS settings was reset, I am able to see the BIOS settings, I will turn off CSM and set my SSD as the bootable device

Try gen 2 mode.. I remembering reading that for my asus Z97 board back when but it was for older graphics like the 980.

Also is there an auto setting for CSM?

Asus has a forum as well.. can't be the only person using a 1060/1070/1080 card in this board.

Also try emailing asus support with the info you tried and see if they know.

Must be wearing out that pcie slot swaping cards all the time. Heh I remember what a pain it was recently when I had 2 1080 ftw hybrids.. what a pain shaping them over and over testing ea card and having to mount and under mount that rad. Sucks.

You did clear the cmos by removing the mb battery for 10 mins to make sure it's clearing the old settings?

I'm doing things slowly now:
Reseted the UEFI BIOS settings of my motherboard by pulling out the battery and doing a power cycle.
Now I can see and access the motherboard's UEFI BIOS settings (CSM auto, the 1080's legacy BIOS loads, but my M.2 PCIe SSD requires it to be off, so I'm stuck in the BIOS settings and can't boot into Windows).
I turn off the system just to make sure that it still works, and I turn it back on, and nothing has changed.
I setup RAID, default boot device, fan settings and restart the system to make sure that it still POSTS, and it does (At this point CSM is not disabled)
Now in order to boot into windows I turn off CSM, since all of my components have a UEFI BIOS, and the 1080 HAS a UEFI BIOS. By disabling it windows secure update and secure boot is enabled automatically.
I reset the system, I hear beep beeep beeep beep, the monitor does not detect any display, and the red VGA_LED is lit all the time.
Windows loads, and after it loads it automatically loads the display driver thingy and I can see Windows now.
I shutdown the system to see if it still posts after a shutdown, and it does.
I restart the system to see if it still posts after the restart, and it does.
Now I cannot access the motherboard's UEFI bios settings, safe mode, advanced startup settings.
 
Again, the 1080 should not require CSM, CSM enables compatibility for older non UEFI compliant devices, and the 1080 should have a UEFI GOP compliant BIOS. enabling CSM loads the legacy BIOS of the card. from what I see the card's UEFI BIOS does not load, that's why there's no display before the driver is loaded I suppose.
 
Also, the evga 970 superclocked in the same system, same configuration, same lane, does not have this issue.
 
I tried the advanced startup option, and now I have a black screen, VGA_LED stays lit, but no beeps, and display never comes on now. I will have to reset the UEFI BIOS settings again I guess. I now know that if it doesn't beep, then it will fail to POST

So it sounds like the easy solution would be to either get rid of the m.2 drive and use a regular ssd for your os and use the m.2 drive for other stuff.

Or upgrade the while system mb/cpu/ram to something like a z170 chipset where you won't have this issue.

Sounds cheaper to move the os to a standard ssd drive and finally use the pc and game.

I got a new Samsung 950 pro 512gb and yeah what I've read that you won't really notice the speed difference from it over a regular ssd drive is basicly correct in everyday use.. for rendering videos yeah there's a difference but one could just move that software to the m.2 drive and be fine.

I didn't have this issue with my maximus hero vii z97 system with a 1080 upgraded from a 980 but I wasn't using the m.2 drive.

AHowes
So it sounds like the easy solution would be to either get rid of the m.2 drive and use a regular ssd for your os and use the m.2 drive for other stuff.

Or upgrade the while system mb/cpu/ram to something like a z170 chipset where you won't have this issue.

Sounds cheaper to move the os to a standard ssd drive and finally use the pc and game.

I got a new Samsung 950 pro 512gb and yeah what I've read that you won't really notice the speed difference from it over a regular ssd drive is basicly correct in everyday use.. for rendering videos yeah there's a difference but one could just move that software to the m.2 drive and be fine.

I didn't have this issue with my maximus hero vii z97 system with a 1080 upgraded from a 980 but I wasn't using the m.2 drive.

This is not a solution .
The EVGA GTX 1080 FTW Hybrid should have a UEFI GOP compliant BIOS. Telling me to downgrade my system to legacy bios to support "older devices like the 1080?" and get rid of my fast and expensive SSD is not an option. I'm not buying another PC/system/components anytime soon, and it will not be cheaper, I expect the 1080 that I just bought to work as it should, it is compatible with the system, so it should work. the EVGA GTX 970 SuperClocked works just fine!
 
Also, if the UEFI BIOS has issues, changing the CPU/RAM/other things wont fix a thing... card not working? buy another cpu, ram? 

Just to let you know your not the first person that is having issues getting a pascal card to work in a older mb. The bios are different then the old 900 series.

Youvery already said over and over you can get to the bios if you enable csm but can't get the m.2 drive to boot then. With it off you can boot but can't get into the bios.

Answer is which one you want more the m.2 drive or the 1080?

Contact evga customer support.

Though prob the only thing that will convince you is going with another brand card and have the same issues.

If you have a microcenter/bestbuy close by it wouldn't be hard to grab another brand 1080 and test.

And why wouldn't it fix it?? I don't have your issue using a Asus maximus hero VIII alpha and I am booting with a Samsung 950 pro 513gb m.2 card with 1080 sli classified cards.. water cooled custom block. First boot I'm in the bios and then off installing win10 pro 1607. Never changed any settings in the bios other then my ram to xmp.

I can't easily swap out my water cooled cards if I had an issue.

Best thing to do at this point would be to contact evga to see if they may be able to fix your issue with a vbios update. http://www.evga.com/about/contactus/