It worked! *EDIT after further tweaking start up is 15s shut down is 10s. This coming from 47s start up and dam near maybe even more than a 1 minute shut down.
 
Micro 2 - 950 Pro - Windows 10 Home 64 Installation Method I used:
 
Here is what worked for me, try this at your own discretion: 
Disconnect everything but your destination boot drive
Put Win OS USB in USB3.0 port
Enter Bios and Restore Defaults
 
----Boot
Quiet Boot ON
Fast Boot Off
Boot Mode Select UEFI
Boot Option #1 USB Key
I think I left Network as #2?
 
-CSM Config
Enabled 
UEFI
UEFI
UEFI
 
----Advanced 
-PCIe Config
I put everything at Gen3 but not sure is it makes a diiference than having them set on Auto
 
-Onboard Device Config
Everything Enabled
 
Save & Exit tab
Save Profile as 'thank you drpower'
Save Changes and Reset
Install as normal
Restart after installation, enter bios pressing F2 and/or Delete
Change Fast Boot to On and arrange the Boot order - Boot drive as #1 Network UEFI as #2
Save and exit tab
Save Profile as 'EVGA is #1'
Save Changes and Reset
 
Shut down unplug the power and install other Sata storage if you have them, go to bios on start up and add them to the boot order.

Just reinstalled Win 10 again and I honestly regret it! My booting time increased from 10 to 70s on Samsung SM951 NVME. My settings are exactly the same as yours using Micro 2 MB. I also tried adjusting the fast boot power option, multiple driver, BIOS, Windows updates and this is getting frustrating. I will switch back to 8.1 if this continues. At this point my WD HDD will boot probably a stable version of Windows faster than my NVME SSD this is ridiculous. 

I'm pretty sure that it is something to do with memory training loops. It takes about 60s on the X99 post screen, then the OS itself is another 7-8 which is not too bad. With win 8.1 it was <15s all together! 
I agree that everything from the boot order and active SATA ports will not improve boot time but it is disabled anyway.
I updated the BIOS 2.02 twice, I also tried reverting back to 2.01 same story.
Magician does not support OEM SM series so it is pretty much useless. I checked the drive with other tools for bad sectors it works fine 2.2GB/s seq read, 1.3GB/s seq write a bloody OS shouldn't be that hard to read. 


Win 10 has it's own issues but this looks like a firmware issue to me. Just wondering why it appears now after several fresh installs :D

IvanLazarov
Right... with single memory DIMM installed (4GB) single channel it boots for 13s from power up to desktop.
with two DIMMs (2x4GB) it boots for 35s.
with all 4 DIMMs in quad channel it takes 70s ...

Why EVGA...Why :D 

I have an SM961 and boot time is about 10 seconds. Was it always this long or was it shorter at any time?