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.
 
 

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. 

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/ 

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?

arestavo

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.

A Test that csrikant can do!
 
Also this MB only has 3 PCIe Slots "X99-MACRO 2 PCIE slot4 not working non of the device are recognized in windows bios show"

csrikant
M.2 is my boot drive I need to reload OS  in HDD to test seems annoying task see my build need to remove Water-cooling stuff to access my m,2
Let me try

See if you can disable it in the Bios before you remove it. Not sure if that really would work through.
Are you also saying that your Wireless card also will not work in Slot 3?

ok removed M.2 /disabled in bios Slot 3 works all devices are recognised.
Final conclusion
Slot 3 is wired to /shared M.2 so if you install M.2 device. And enable in bios M.2 slot  Slot3 is disabled  will not recognize any device in windows.
 
 

I still happy with this system I have ASUS MATX M-WS same CPU and RAMS can get only 4.5 MHZ overclock
EVGA can get 5.2MHZ overclock so happy to live with this build move my Intel drive to ASUS and use this system like this.

csrikant
ok removed M.2 /disabled in bios Slot 3 works all devices are recognised.
Final conclusion
Slot 3 is wired to /shared M.2 so if you install M.2 device. And enable in bios M.2 slot  Slot3 is disabled  will not recognize any device in windows.
 

This is what I was thinking.

The way the PCIe Controllers are in the chips limits the way it can function.

The 40 lane chips can have up to 5 blocks of x8, 4 blocks are used in the top two x16 x16 slots, leaving the last 8 lanes for either Slot 3, or the M.2 slot.

The 28 lane chips have 3 blocks of x8 and 1 block of x4, the 3 blocks of x8 are used in the top two x16 x8 slots, then the last x4 block is left for either Slot 3 or the M.2 slot.

Without more sophisticated PCIe lane switching (which would take up more board space, increase latency, is more complex to design around and a whole host of other things), having both functions available at the same time is a no-go.

Just be happy that the M.2 slot runs at PCIe 3.0 x4 unlike a lot of X99 motherboards which only use 2.0 x2/x4.