What case and cooling are you using with two GTX 1080's?
 
 

I will fire my 1080 up and see what they can do as far as PPD. (Driver 373.06)
I am seeing 724870.8 (Long Run P11418) and 745699.6 (Short Run P9191)
 
I would do this: (Unplug network cable or turn off your Wireless network)
Remove NVIDIA Divers
Reboot PC

Run DDU in Save Mode
Reboot PC

 
Using the Registry Editor Delete:
Win7
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Video
HKEY_LOCAL_MACHINE\SYSTEM\ControlSet002\Control\Video
Ignore the Errors
Reboot PC
 
Win10
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Video
Ignore the Error
Reboot PC
 
Install 373.06 Graphics Drivers
Reboot PC

 
X79 If not Gen3 (Under NVIDIA Control Panel) then Run force-enable-gen3.exe
Reboot PC

bcavnaugh
I will fire my 1080 up and see what they can do as far as PPD. (Driver 373.06)
I am seeing 724870.8 (Long Run P11418) and 745699.6 (Short Run P9191)
 
I would do this: (Unplug network cable or turn off your Wireless network)
Remove NVIDIA Divers
Reboot PC

Run DDU in Save Mode
Reboot PC

 
Using the Registry Editor Delete:
Win7
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Video
HKEY_LOCAL_MACHINE\SYSTEM\ControlSet002\Control\Video
Ignore the Errors
Reboot PC
 
Win10
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Video
Ignore the Error
Reboot PC

Install 373.06 Graphics Drivers
Reboot PC

 
X79 If not Gen3 (Under NVIDIA Control Panel) then Run force-enable-gen3.exe
Reboot PC

I actually did all this prior to installing the new cards.  When I had the old card, it was a fresh install of windows.  It's frustrating as the MSI card is destroying the FTW, literally.  I'm going to give it another few days and then I am going to swap the cards around and see if it's a slot problem.  Currently the FTW in slot 1 is making 569k ppd and the MSI is making a whopping 863k ppd.  All tests show that the cards and slots are in pcie 3.0.  I won't know the real truth until I get some some similar work units on each card to see if it truly is the case.  And it's not like I don't have the pcie lanes.  E5-2670 has 40 of em, and there is nothing else in the slots on the motherboard.
 
Both cards are still running below 80C and are still boosted well above stock.

In my BIOS they are showing PCIE 3 as well.  As I said the MSI card is performing as it's supposed to, it's the FTW, like the previous FTW, that is performing horribly.  I figure at this rate, if I give it a few more days, then swap cards, and if the FTW performs the same in the slot the MSI is in, then I know for sure something is up with the FTW.  However if the MSI does the same horrible jobs as the FTW does in the primary slot, then I know it's time to RMA this board as there is something wrong with the slot as it's not working properly at all.  A couple more days will also give me a chance to get more work units to compare the 2 cards a bit better.  I hope.  Just frustrating that I can't seem to get what the FTW is supposed to get.

Using precision x.  Had the card set on stock settings.  When the card is solo, it refuses to boost half the time.  I am at my wits end.  If I have both cards in the system, after a day of folding they both start going at about 900k ppd.  But solo, the 1080 FTW just sucks.  Right now it's going at 1721, and I have it set to overclock at +50 on the gpu and it's not even doing that, just sitting at stock speed and ignoring the overclock setting.  Temp is a cold 50C.  I'm about to ask for another RMA on the card as I've had it reboot my system several times while folding today and yesterday causing me lost points from "bad work units" when the card wasn't even hot, at only 65C.  It will be my second FTW that's bunk.   Beginning to regret having bought a B stock unit at this point :(.
 
The MSI is currently in my son's rig as he was complaining his 970 wasn't able to handle Resident Evil properly.  So until he can save up to buy a better card or buy the game on xbone he has my other card.
 
My room is usually around 20-22C and at night it's even colder as I keep my window open.

And now the stupid card is working properly.  I swear this thing has a mind of its own.  Boosted to 1987 with a temp of 67C and getting 903k ppd.

No cause my machine was going great when I had both cards in, both doing over 900k ppd for a few days.  Then when my son needed a new card and I lent him mine, my FTW went back to folding like a 1070.  Unless it's all the stuff over at Stanford and their server issues that's causing this.  Though I do find it weird how when I woudl tell the card to overclock it wouldn't, even when I would try to run a benchmark, a different mining program like marlin, or even folding.  And now after sleeping, the card appears to be working fine.
 
I don't know if I should take a baseball bat to my computer or what!@$  I am so frustrated with how inconsistent it's been lately.

Wow... Actually after doing some research on my cards.. both my 1080s are hitting below 700K in PPD.    I have a FTW and a G1 OC..    

Running 373.06.  

Grr might need to make my next purchase either a 1070 or a 1080ti.  The 1080 sucks for ETH mining and now it sucks for folding lately.  Why have you forsaken us NVIDIA, why?

When I had 2 cards, they were both averaging almost 930k ppd according to HFM, but as soon as I went down to 1 card, I am back down to 650k or less ppd.  I had to lend a card to my son so he could play his games as my old 970 was "not cutting it".

I have reset the bios multiple times.  But I will do it again.  :)  I have the right passkey, and the projects I keep getting SUCK.  I think that might be the issue.  When I had both cards I would constantly get project 13204, now all I seem to get is 11428 600+ppd or 10496 500+ppd.  I've only gotten project 9415 5 times since May 1st.
 
my slot is set to client-type advanced, next-unit-percentage 100, max-packet-size big.
 
Oh and speak of the devil a 13204 just showed up and my current ppd is 932807.  Wish this was the only work unit I would get...
6% complete
Base 13541
Estimated Credit 85525
Estimated ppd 923667
tpf 1 min 20 sec
 
Clocks are currently GPU 1974 Memory 4959. Temp 75C