Here are my BIOS settings if anybody else is having an issue.
Before you start, have only the M.2 drive connected.
Set BIOS to defaults and restart. Back in BIOS, set SATA mode for ports 0/1/2/3/4/5 to RAID, set SATA mode for ports 6/7/8/9 to AHCI, enable the M.2 port, check that Launch Storage Op-Rom is set to Legacy, F10 and restart, back in BIOS one more time, click BBS priorities to see if the drive is listed for boot option #1.
 
This is all I had to do. I'm guessing the big issue was the old firmware.

*** Step one is to make sure your Samsung M.2 SSD has the latest firmware using Samsung Magician ***
 
First page showing BIOS version (the x4 2.0 in the PCI-Express section is my M.2 drive).

 
Second page showing SATA ports 0/1/2/3/4/5 set to RAID

 
Third page showing M.2 socket3 enabled.

 
Fourth page showing Launch Storage Op-Rom set to Legacy.

 
Fifth page showing Boot Mode Select set to Legacy.

 
Sixth page showing Hard Disk Drive BBS Priorities (Boot Option #1).

 
 
 
 
 

bcavnaugh
 
I missed the #3 Socket 3.

Are you referring to the Intel 486?

HeavyHemi

HarryD

bcavnaugh
 
I missed the #3 Socket 3.

Are you referring to the Intel 486?

3rd image, M.2 Socket3

Yes
 
But I did have a 486DX CPU back in the day.

Great job Harry.  
 
On my XP941, my M.2 wouldn't show up unless I had UEFI enabled.  If anything, these type of steps could be just needed for the newer M.2 PCIe SSDs while the older ones needed different conditioning.  This just shows how finicky M.2 gets on X99.

Nice work Harry! There is a little hope for the X99 boards supporting M.2 SSD's. But you still have to jump through a lot of hoops to make it work. But being insistent pays off!
 
I'm still waiting til the M.2 tech is more standard to motherboards, as SATA drives are.

Wondering if I should make a how-to and maybe have EVGA make it a sticky.

GTXJackBauer

bobmitch
Some years ago, if anyone remembers the Promise RAID controller...you would hook the two hard drives up to it and when you went to install Windows...couldn't see the drives until you did the same thing with it's driver.  Not finicky...we are just at a time, when only Windows 10 and Windows 8.1 later builds recognize M.2 with no problem.

We can agree to disagree.  I've been around long enough to remember IDE/SCSI.  Still have those laying around.

RAID is a whole other beast of its own.  Here, were just talking about simply connecting a drive to the PC to first, recognize it in the BIOS and second, being seen by Windows for installation.  Back in the day, all you had to do is hook up the cables and make sure your boot order was up to speed.  Once we transitioned to SATA HDs and SATA SSDs, same thing.  M.2 is in it's own world is the point for the time being.  As Brock said, he'll stick around till M.2 becomes more of a standard and all the bugs have been worked out.

I had a Promise IDE controller as well.  In order to get the machine to boot to it, I had to add "external card" or the like in my boot order...then install the drivers. 
 
 
https://www.newegg.com/Product/Product.aspx?Item=N82E16816102027
 
 
At the time, they were considered much faster than the IDE bus on Intel motherboards. 

Oh c'mon. Setting SCSI was trivial. At least my humble person never run into problems. Jumper fun. Stopped with SCSI at UW160. 320 was not good enough and far too expensive in the long run - with  most devices hardly capable of saturating 160 interface let alone 320 (bit like modern VGAs). 
 
Oh I remember bags of terminators lying around, cables of every imaginable sizes and connectors. It was right old mess at some stage, especially if everything was run externally.

HarryD
I've never had the pleasure of working with SCSI. IDE/PATA is as far back as I go with drives and jumpers.

SCSI was never intended for use by casual home user, but it was quite popular anyway. Controllers alone were somewhat expensive for starters (especially later when UW introduced 68/80pin connectors). But you could get stuff for fairly reasonable amount of $ on short notice. There was also a lot of peripherals which worked on SCSI architecture. Scanners are most obvious example. Especially if wanted A3 you had to go SCSI. Also CD-ROMs, MO drives. I remember my first PC. It was equipped with 5.25" 600 MB Fast SCSI HDD. I still have it few steps from me. It sounds like a broken turbocharger when powering up and like crashing airplane when powering down, but hey, mid '90s I could hold data for whole of my street combined - not that many people had computers at that time. Still in working order, but keeping it purely for sentimental value.
 
Same as SAS today, but with SAS they went overboard and totally 'bananas' price-wise. While you can get new controller/expander just fine - it will cost you 500-1200$ -, SAS drives are ridiculously expensive, each can cost much, much, much more than controller alone - especially SSDs and I don't even talk these behemoths of 13 or 15 TBs, but puny 480 GB. And that's why you get SAS card and then plug SATA devices to it. Because you can and it's infinitely cheaper option. :)

HarryD
Windows is reinstalled to the M.2 drive and everything is working normally. I'm installing programs and games as I type this.

That's great news.  

Congrats on M.2 working

third pcie slot disabled due to 28 lanes in use