Can we get a full system spec please, that would be helpful.
Have you already installed an OS at this point, if so what OS?
What, if any, BIOS changes have you made?
Have you verified that the M.2 is enabled in the BIOS when you are seeing these issues?

I assume you are using the M.2 slot, not a PCI-E based adapter to attach your M.2 device?
Assuming you are on the native M.2 slot, what speed is your RAM?
Make sure it is not set above 2666 (done by adjusting BCLK to achieve RAM speed) as that will cause a conflict with the M.2 device.  This is part of all BIOS's since 1.01.

I've got the Samsung SM 951 m.2 on the same motherboard and no problems here on the 1.02 BIOs.
 
This is the item I bought: http://www.ebay.co.uk/itm/Samsung-SM951-256GB-M-2-Solid-State-Drive-/111675090438?
 
Did you format the M.2 for GPT with the motherboard BIOS set to UEFI?
 
 

Unsure if it should make a difference, but I decided to join the 21st century, and did a complete EUFI-compatible installation, and confirmed the M.2 was now GPT.   Only BIOS changes were to enable M.2, and EUFI boot.
 
Several reboots and no issues.   Tweaked a few further things in EUFI - all of minor consequence.   Set RAM to XMP1, which is 2400 MHz at 1.35V.    A couple more restarts without issue.
 
Decided to try a cold boot - grrrrrr - M.2 drive not detected again.   Had to restore defaults.  :(
 
 
Any other recommendations?   RMA at this point? 
 

_phlegm_
2 more cold boots.   First one the M.2 not detected.   Next one the M.2 is detected.
 
Default BIOS settings (aside from EUFI boot/enable M.2), so will await other ideas, or RMA suggestion.

make sure to disable fast boot. You can also try disabling CSM.

I've confirmed an M.2 drop issue with this board.   100% of cold boots fail to pick up the M.2 drive:
 
1.  It boots to BIOS.
2.  I restore defaults.
3.  I enable M.2 and EUFI boot.
4.  I save changes and restart.
5.  I successfully boot to windows.
 
If I shut down the machine, the M.2 drive is not found, and upon entering the BIOS only the X16 PCIe of the GPU is shown, and the X4 for the M.2 is no longer there.   M.2 continues to be enabled in the onboard devices submenu, so it's not like that setting is getting changed/lost somehow.
 
In each case, repeating steps 1-5 allows me to get into Windows.   So while I would almost suspect the SSD, it is resolved 100% of the time by a BIOS reset.   Also, as mentioned, I've used the same drive in another machine for several months now without issue.  (I still have the barebones of that setup now, and can test it, albeit with some pain & difficulty in swapping some things out.)
 
Fast boot is disabled by default, so that's been the setting for some time now.   CSM is enabled by default, but disabling it for 2 cold boots did not help unfortunately.
 
While I assume I had done several cold boots yesterday, I probably only did a couple of them, and had 2 failures to boot that I recall.   This morning my first boot was also a failed load, so the issue is the same as I first reported.   Warm restarts never show the issue.
 
I suppose RMA at this point?
 
 

Hey, I appreciate all ideas.   Board shipped with 1.01, and I flashed to 1.03 yesterday - no change.

Thx for the reality check Dave.
 
Yesterday morning, I turned on the machine for the first time, and was ready to jump into the BIOS for a reset, but the machine booted normally.   Recall that a couple of days ago I did 7 or 8 cold boots in a row, and every time the M.2 drive was not found.    This morning I turned on the machine just now for the first time, and it also booted as expected.   Strange.
 
I realize faulty components can do random things, but I wonder if there's a pattern here, maybe temperature-related?   Maybe the motherboard, or the M.2 drive itself reacts oddly when at a certain temperature?
 
As mentioned, I never had a boot issue on my previous motherboard, and it was a cramped ITX build.   However, the M.2 was installed via an NGFF slot that was perpendicular to the board - decent exposure for ventilation.   I only had a 120mm case fan in that build, but it was blowing directly at the drive.   In my new ATX build, I have 2 X 140mm case fans blowing at the board (with no drive obstructions), but the M.2 on this board is tucked under the GPU**.   Maybe not quite as good airflow?  
 
It might have zero to do with any of this, and just be defective randomness, but I'll test a bit more, and report back.   I'm just guessing at this point.
 
 
**Can I run a single card setup if I move the GPU to a different slot?   That might help me test airflow on the M.2, but unsure if a single card must be in slot 0 (first).

Nope, it's completely random.   Started the machine after 4 hours off, and drive not found.   Nothing to do with temperature. 

Will definitely give the chipset drivers a try, thx for the idea.
 
As the the M.2 firmware, the SM951 is OEM, and thus I can't find anything specific for it.   I would suspect firmware, except rjohnson11 has the same drive without issue, and my drive was fine on another motherboard.
 
I'll report back on the chipset update...

bcavnaugh

_phlegm_
Will definitely give the chipset drivers a try, thx for the idea.
 
As the the M.2 firmware, the SM951 is OEM, and thus I can't find anything specific for it.   I would suspect firmware, except rjohnson11 has the same drive without issue, and my drive was fine on another motherboard.
 
I'll report back on the chipset update...

Download Samsung Magician Software for PC and let it update the firmware if their is on.
http://www.samsung.com/global/business/semiconductor/minisite/SSD/global/html/support/downloads.html
It also can clean up and fix error on your M2.
 

Good suggestion for the Firmware, as I have had similar with a SATA SSD myself.  However a chipset DRIVER update won't help anything, as the drivers aren't initialize anything until after the OS is loading, if this is an issue at cold boot, then it will not be fixed by a driver update, Firmware and Samsung Magician may well get you up and running correctly though.
 
Let us know how this goes.

_phlegm_
Sadly, Samsung Magician does little for the SM951 given its OEM status.   The drive is merely detected in SM, but firmware updates, Rapid mode, and other goodies are greyed out.
 

Good reason why I cannot find your SM951 on Samsung web site, maybe that is your problem as it was made for the other half of the OEM Device it was made for.
Did the company that sold you the OEM device say that it would work on the X99 Platform?
Or is it a reuse of old hardware?

The XP941 and SM951 were only made for OEM.  Meaning these were made for laptop manufacturers.  They don't carry any warranties on them as a 3rd party warranty needs to be purchased.  Samsung will give you shrugged shoulders if something were to happen.  No software or firmware for these drives.  What you would want to look at is getting the M.2 950 Pro which has a 5 year warranty on it and is recognized by Samsung because it is a non-OEM because its a actual retail product.

I'm experiencing the exact same thing with my Micro2 and retail box 512GB Samsung 950 Pro installed in the M.2 slot. Cold boot - drive not recognized. Power it off and right back on, the drive works perfect. I believe this is a BIOS issue. Once booted up and working, everything is normal, with great speeds. Warm reboot, still works. For now, I'm just powering my computer on in the morning, powering it off, then back on.. until a proper BIOS version is released.
 

Tried that as well. Still not working. I also have sleep disabled.