• The win10 update is no bueno for machines that aren't stock.  I had a lot of small issues.  Nothing that wouldn't have been ok if all this machine did was surf the web.  Clean win10 install had to be done. 
• I am getting a lot of monitor flickering and ghosting on the new 980ti sc+ (4995) when I use the top left (when looking at the monitor connection side of the card).  Happened both when using the upgraded win10 and now the new install of win 10.  
  • by flickering I mean that the monitor will go black (for a couple ms) varying from 1 to 3 times, like bam bam bam.  Sometimes after that I will get ghosting.  By ghosting it looks like all the text, icons, etc are offset a couple of mm's.  The text is really illegible, but since I know what I need to click and where it is I can just restart and it looks fine and then an hour or sometimes 5 mins I get the flickering  and then ghosting etc.  This happens both while on the desktop and in games. 
  • This flickering has happened in both the single card and SLI when this card is in the top slot. 
  • Also when in bios and when booting sometimes the signal is there and then it drops.
• When I use the display port that is to the immediate right of the top left. I don't have many issues but occasionally I will get a flicker when coming out of a game. Haven't seen any flickering in games, just on the desktop coming out of a game. 
• With my vanilla 980ti (4991) and use the top left displayport the monitor doesn't sense a video card.  When I use the displayport on the immediate right of the top left.  Video is detected.  In Win 7 and then in the upgraded win 10 I did get some display port flickering like above, but no ghosting. Both on desktop and in games. Also when I use this card in the top slot the temp difference is approximately 10 degrees c.  When this card is in the bottom slot about 2-3 degrees c. I have an occasional flicker while in desktop.
• Using the current hotfix driver (368.51) also happened when using 368.39.
• Installed a new EVGA 1000 P2 powersupply
• When using the cards in SLI I cannot use any other displayport other than on the top card.  I listened on a youtube video with an Nvidia guy that states that you should be able to use any displayport and that it would reduce some heat on the top card if you use a displayport on the bottom card.
• DVI works all the time.  No card detection issues, no blank screens after flickering, no signal issues in the middle of the bios.  If I have a no signal issue and then connect a dvi monitor the screen comes back.
• Have tried two displayport "certified" 1.2 cables.  Same issues on both.  10' length.  Have a third on order and should be here tomorrow.
• Refresh rate is at 144hz at 1440p.  Have not tried lowering refresh rate and seeing if the issue still occurs, but I shouldn't have to.

arestavo
Have you tried the latest hot fix drivers? They supposedly fix desktop flickering.

http://forums.evga.com/Ge...er-36851-m2499007.aspx

arestavo

• This flickering has happened in both the single card and SLI when this card is in the top slot. 

So, on one of the cards this doesn't happen? If that is the case, then you've got a faulty card and it is time to RMA.
 
Have you tried:
 
A different port on the monitor? (I couldn't tell for sure with your description)
 
A different DP on the top GPU? (I couldn't tell for sure with your description)