I have X99 macro2 MB
I have issue in slot 4 devises or not recognised in windows.
Bios show slot occupied withX4 device but noting seen on device manager. Scan Hardware. changes do not detect any HW change in windows
Am using W10X64 Enterprise. CPU I7-6850K (40 lane Cpu) Ram Ripsaws5 3200Mhz 11-14-14-34 HDD Intel P600 M.2 slot occupied by OS.
 
 

Welcome to the forums!
 
What PCIE device (s) have you tried is slot 3? (Slot 3 is what the manual shows as the bottom slot)
 
And have you updated to the latest BIOS? Edit: It looks like 2.02 is the latest for the Micro 2.

yes bottom slot3 as pic above
Devices work on slot 2 but not on slot3.
Device I intend to use is intel 750 series 1.2 TB NVME ssd doesn't work. But works on slot 2.
But I have intel Wi-Fi card  7260 in slot 2 for currently using  as I need Wi-Fi and Bluetooth for my Head phone and printer. 

bios update 2.02 still the same issue

You can try to use compressed air to blow out the PCIE slot. There may be some dust or debris causing this issue, and you might be able to use a flashlight to see the culprit.
 
You may also want to check the CPU socket for bent or broken pins.
 
Other than that, I'm thinking it might be time to call up or email EVGA to see about a RMA: http://www.evga.com/about/contactus/ 

PCIE slot seems clean
Am no sure about cpu socket but I did check before building it was clean and no bent pins everything works fine in the PC except slot3 does recognize devices in bios but it does not show up in windows device manager. I did fresh install to check the issue it still same issue with to slot 3.

I see you have an M.2 Plugged in, remove it and your slot 3 should then work.
Also have your Re-set your Bios by Holding down the small read button for 5 or 6 seconds and then enter into the Bios and check to see if your device is showing up?

bcavnaugh
I see you have an M.2 Plugged in, remove it and your slot 3 should then work.

I looked for that in the Micro 2's manual, but didn't see anything saying that a PCIE slot is disabled with m.2 plugged in - 28 or 40 lane CPU.
 
Edit: I was wrong, and I missed that it SHARES PE3 (aka slot 3) (kinda stupid to have that limitation with a 40 lane CPU and only 3 PCIE slots):
 
Expansion Slots:

1x M.2
-M.2 Socket 3 (Key M), M.2 needs to be enabled in BIOS
 
as it is shared with PE3.
 
M.2 uses PCI-E 3.0 x4, with speeds up to 32 Gb/s.