I have a 1600W EVGA power supply, a MSI X99A Gaming 9 MB... 
 
I'm adding my second GTX1080 Ti FTW... I confirmed both cards working on their own with out issue. The second I have both in the system the one in the lower slot shows up in device manager with windows error code 43.
 
Thoughts?

Confirm that all PCIe power cables are indeed fully seated - including at the PSU end if it is modular - sometimes they get tight before fully seated
 
Code 43 = Windows stopped your device - reported problem --> [try the following]

1) Select the Start - in search box, type "device manager" (do Not type Quot marks) and select Device Manager from results.
 
2) Find the device in the list (it will often have a yellow "exclamation point")
 
3) Press and hold (or right-click) the name of the device, select Properties. - select the Driver tab, select "Roll Back Driver", then follow the steps. If the button is unavailable, that means there's no driver to roll back to.
 
4) Select "Uninstall device" and then select Uninstall.
 
5) At top of Device Manager, press and hold (or right-click) the name of your PC, select "Scan for hardware changes" - reinstall the device driver.
 
6) To check if its fixed - press and hold (or right-click) the name of the device again and select Properties. Then General tab, under Device status, you should see This device is working properly.

Sounds like you may have a faulty pci-e slot.

Cool GTX
Does that MB have switches, to disable the PCIe slots ?

Nope.

Hmmmm, I switched from a MSI X99 SLI yesterday, thinking that same thing. Same result... This is crazy... Maybe it's the card? But they both work independent. I could switch slots. Keep in mind each card works fine in it's current slot if the other isn't installed.
 
 

Hmm. Sounds like your cpu may have a problem.

He's not trying to sli then together.

Edit.. umm wait. Wrong guy.

Where's the sli cable?

Even still.. I think it's norm to have the sli connector installed even before installing the drivers.. how I always did it.

Sajin
Hmm. Sounds like your cpu may have a problem.

Yeah if the cards work totally fine by themselves in the slots there in currently then the slots work and the cards work. All that's left is either a setting in the bios or time to pull the cpu and check for bent pins.

No idea on the bios settings.. if one need to select 8x8 for the cards or if there's a sata or m.2 drive sharing with the pci-e slit the last card is installed on.