I see you have a nice 960 Pro M.2.  I'd advise on going with a PCIe 3.0 adapter for the PE lanes, otherwise you're capping it at PCIe 2.0 within the interface.
 
Here are the steps I took to setup my XP941 (PCIe 2.0) SSD.
 
- Enable M.2 socket3 (You won't have to if you're going with the PCIe lanes.)
- Enable BIOS in UEFI
- Save and Reboot
- Make sure your M.2 SSD drive is at top of the boot order.
- Should be good to go.

i don't use the m.2 slot on my motherboard, because i found the speed of my 950vnand was really low, this is what i us for my 950vnand https://www.overclockers.co.uk/asus-hyper-m.2-x4-pci-e-mini-adapter-card-black-pcb-hd-032-as.html it just slots in to a PCI-e slot(don't put it in x16 slot), you can pick them up cheaper, think i paid around the £10 mark, avoid the cheap cheap generic ones that are on ebay.
 
I will say that when the 950vnand had been run for a few months and i moved it back to the M.2 slot on the mobo the speeds were greatly increased from what they were before, i would say that all components need time to be bedded in, give it time and all will be well, remember to optimize the drive now and again or set up a schedule for it to be optimized.
 
http://www.samsung.com/semiconductor/minisite/ssd/download/tools.html near bottom of page is the driver you'll also get magician so you can setup the "over provision" and that'll also speed things up greatly, in their, try not use the microsoft one that is nae doubt installed atm,
 
remember to select thing as the boot drive :D + don't hold me on it but have you set all you devices to UEFI and not legacy in the Bios, on my asus mobo i found the the settings in CSM also in secure boot section you want to set that to "other OS"(not windows) and set enhanced mode.
 
you might have to hunt in the bios as yours maybe called something differnent, but you should spot it easy enough,
 
 
 
 
 
 
 
 

arestavo
No, you don't need the m.2 drive to be in a PCIE adapter for it to boot.
 
The only reason to use a PCIE adapter is to get the full PCIE 3.0 speeds - which makes zero difference in game loading and windows boot times: http://forums.evga.com/EVGA-X99-Classified-NVMERAM-DriveRAIDSATA-III-SSD-Game-Load-Times-m2556132.aspx
 
Remove all other drives from the computer and try again. If booting from your cloned m.2 drive still doesn't work, then try installing Windows from scratch (you'll need windows 8 or 10 to have the NVME driver, or you'll need to download it and put it on a disc to load it during the windows install).
 
If that fails to work, then I'd guess that your board has an issue, and I'd call up EVGA and see about an RMA: http://www.evga.com/about/contactus/

yea that the answer RMA, do you hear what  your saying let the @op sort it, afore going on about RMA, this is not hardware related... it's Bios setup up problem
 
or as you say he might be using OS less than 8 or 10 BUT if the OS installed on to the 960 then it sees it then it's a booting issue bios settings needs changing see post 3 and 4
 
but maybe it's a 960vnand problem and maybe the @op should RMA that first would that be more of an idea....?
 
or maybe he should just RMA the lot and be done with it?
 
CSM and change everything to UEFI, or if your not happy changing every/any thing just change the storage to UEFI first option
 
and if you have another install on another boot drive that is attached make sure sure you running the right windows boot manager
 
i'm not slating anyone off but when i got my x99 board i got so frustrated with it that i booted a hole in the perspex side, but when i did a bit of research i released it was me that was the problem, because the bios not being setup correctly. i even thought of RMA option but now I sorted myself I felt kinda chuffed, and proud to say "this is my board" they don't call it a "enthusiast" board for nothing,  
 
 @op if you feel in yourself, that you have given yourself enough time to sort it out, try phoning support or dropping them a email to see what your options are, but do it out of frustration do a bit out research plenty online google is your friend :)
 
maybe has nothing to do with it but remember to change your system agent voltage to 0.350v and cpu vin to 1.95v and booting becomes less of an issue
 
THEY DON'T CALL IT A "ENTHUSIAST" BOARD BECAUSE IT'S PLUG AND PLAY, if you wanted one of then maybe you should have gone for a "consumer" board.. respectfully :D

hey lookk at it this way at least things are moving forward :) 
 
 
do an install with it still set in UEFI mode, change everything to UEFI first i.e graphics, network and blah blah, have you got CSM turned on? try clearing the secure boot keys this could also be issue
 
mine and report back :)
 
P.S i have asked Sajin one of the moderators to have a look at the @op see what he thinks
 
 
 
 
 

OK, here's where I'm at.... Tried every combo. Still system hangs when trying to boot from UEFI.
CSM Configuration:
   Launch PXE OpRom Policy          UEFI
   Launch Storage OpRom Policy    UEFI
   Other PCI device Rom priority   UEFI 
Fixed Boot Order Priorities
   Boot mode select                     UEFI
 
Tried booting with all this selected without drive installed. System still will not boot into windows. Hangs at Classified X99 Boot screen. So this tells me it's not the drive. Still have to turn Boot mode select to Legacy!
 

I did reset my defaults. This is frustrating. Wanted to Migrate my main system to this new 960 M.2 drive. Just not happening. I sure don't want to get a new board for one M.2 SSD. Would be silly, besides I have had this X99 Classy for just one year this week.....
 
Place Purchased: EVGA
Purchase Date: 11/27/2015
Date Registered: 12/12/2015 9:09:44 PM
 
I haven't given up yet. Thanks for all your help everyone. Happy Thanksgiving... I got to get to the Gym and let out some frustrations!

All X99 boards are not the same. This round the manufacturer was 100% responsible for the BIOS and compatibility, unlike the X79 and X58 platforms which were wholly or partly based on the server board equivalent and had much better compatibility for add in cards.

baconinabun

arestavo
All X99 boards are not the same. This round the manufacturer was 100% responsible for the BIOS and compatibility, unlike the X79 and X58 platforms which were wholly or partly based on the server board equivalent and had much better compatibility for add in cards.

i'll would correct on a few thing no one said it had to be in the pci-e complex to boot, bit silly having a m.2 port if it ain't going to be able to boot from and i still don't agree with you on the x99 situation BUT what i'll do is get a hold of x99 evga board to play with for a bit and get back to you :) 
 
i notice on mods rig you rocking a 950pro in the pci-e complex, is there a reason you don't use the m.2 slot? if your board has one what issues did you have and how did you address them?

Originally I wanted to have the "best and fastest" - knowing that the X99 Classified had PCIE 2.0 for the onboard m.2 slot I went and purchased an expansion card to get PCIE 3.0 speed. That turned out to be completely unnecessary as game loading and windows boot times are almost exactly the same as my SATA III 850 EVO SSD, and I did a post about it and included the few other reviewers that bothered to test normal usage as well - http://forums.evga.com/EVGA-X99-Classified-NVMERAM-DriveRAIDSATA-III-SSD-Game-Load-Times-m2556132.aspx
 
I did not have any issues getting the drive to work with the expansion card - popped it in, used Samsung's migration software, took out the old SATA III SSD, and it booted into Windows 10 just fine.
 
If I get the chance Saturday night or Sunday, I'll remove the 950 Pro and try it in the m.2 slot of my X99 Classified. Since one of the m.2 slots takes away a USB 2.0 port, I'll be using Slot M which takes away PCIE slot 5. Which, come to think of it, might be the OPs problem since there are two different m.2 slots (one meant more for WiFi cards as it is slower (slot E), the other for storage devices (slot M)).
 
Expansion Slots:
5x PCI-E 16x slot 2x16/8, 3x8, 4x8
1x PCI-E 4x slot
2x M.2 Ports
-M.2 Socket 1 (Slot E) shares signal distribution from USB2.0 #3 port,
please select the operational mode in BIOS setup menu
-M.2 Socket 2 (Slot M) shares signal distribution from PE5, please select
the operational mode in BIOS setup menu

Now I tried selecting UEFI.
 
Boot Option #1 to USB Key (Win 10)
 
Then boot into Windows install. The list of drives to install Windows 10 still did not reveal my 960 M.2 SSD. Just listed drives already on system. No matter what I do. My X99 Classy will not see the M.2 drive.