I can replicate a warning in my event viewer on windows 7.  It gave me 15,000+ errors in the last 24 hours. I have 680s in SLI and both are running in 16x with a sound card on the bottom slot  running at PCIE 2.0.  I get this error if I have pcie 3.0 enabled in the bios.  If I enable the video cards to pcie 2.0 in the bios  I can get the error to go away.
 
I'm also experiencing stuttering during gameplay in a simple game such as Counter strike global offensive.  I've never experienced such stuttering with my x79 setup.
 
 
A corrected hardware error has occurred.

Component: PCI Express Root Port
Error Source: Advanced Error Reporting (PCI Express)

Bus:Device:Function: 0x0:0x3:0x0
Vendor ID:Device ID: 0x8086:0x2f08
Class Code: 0x30400

The details view of this entry contains further information.

Something is wrong with the board or CPU.

With my 280x set to PCIE 3.0 I am getting a WHEA bluescreen referencing PCI express. Setting it to PCIE 2.0 seems to have resolved the issue. I think there may be a compatibility issued between PCIE 3.0 and some devices. I have tried updating the firmware of the card, updating the BIOS and installing the latest chipset drivers. I have also tried different video card drivers.

I'll report back shortly.

Dear bigmyke and nainkaigo,
 
I have escalated this thread to my product management team for further review.
 
 

It happens on 1.06.  Which bios version should I try?  I instantly flashed to the latest bios when I got the board and before I noticed the event errors occur.  should I wait for the next bios to release?

Is it starting to look like our boards with these problems are needed to be RMAd?

I have a debug log of the problem if it is helpful. I looked up the device and vender ID and it points to the Haswell-E PCI Express Root Port. After setting my PCI-E slot that the video card is plugged into I haven't had a problem, but that isn't really a fix. Here is the full debug log if it is needed:
 
******************************************************************************* *                                                                             * *                        Bugcheck Analysis                                    * *                                                                             * *******************************************************************************
WHEA_UNCORRECTABLE_ERROR (124) A fatal hardware error has occurred. Parameter 1 identifies the type of error source that reported the error. Parameter 2 holds the address of the WHEA_ERROR_RECORD structure that describes the error conditon. Arguments: Arg1: 0000000000000004, PCI Express Error Arg2: ffffe000e371d038, Address of the WHEA_ERROR_RECORD structure. Arg3: 0000000000000000 Arg4: 0000000000000000
Debugging Details: ------------------
BUGCHECK_STR:  0x124_GenuineIntel
CUSTOMER_CRASH_COUNT:  1
DEFAULT_BUCKET_ID:  WIN8_DRIVER_FAULT
PROCESS_NAME:  System
CURRENT_IRQL:  9
ANALYSIS_VERSION: 6.3.9600.17237 (debuggers(dbg).140716-0327) amd64fre
STACK_TEXT:  ffffd000`2c938e08 fffff800`a1bd8213 : 00000000`00000124 00000000`00000004 ffffe000`e371d038 00000000`00000000 : nt!KeBugCheckEx ffffd000`2c938e10 fffff800`a15d8825 : 00000000`00000001 ffffe000`e35ef100 ffffe000`e35ef100 ffffe000`e371d038 : hal!HalBugCheckSystem+0xcf ffffd000`2c938e50 fffff801`0ef1a64b : 00000000`00000750 00000000`00000001 ffffe000`e35ef084 ffffe000`e35f09d0 : nt!WheaReportHwError+0x22d ffffd000`2c938eb0 fffff801`0ef1af9e : ffffd000`2d116a00 ffffd000`2c938f50 ffffd000`2c900180 00000000`ffffffff : pci!ExpressRootPortAerInterruptRoutine+0x257 ffffd000`2c938f10 fffff800`a14e73e2 : ffffd000`2d116a00 00000000`00000000 ffffce49`e28aa1b1 00000000`0000000c : pci!ExpressRootPortInterruptRoutine+0x22 ffffd000`2c938f70 fffff800`a156d1e8 : ffffd000`2d116a00 00000000`00000000 00000047`720f18c9 ffffe000`e3ea69c0 : nt!KiCallInterruptServiceRoutine+0x122 ffffd000`2c938fb0 fffff800`a156d53b : 00000000`00000000 00000000`00000000 00000000`00000000 00000000`00000000 : nt!KiInterruptSubDispatch+0x108 ffffd000`2c92a750 00000000`00000000 : 00000000`00000000 00000000`00000000 00000000`00000000 00000000`00000000 : nt!KiInterruptDispatch+0xfb
STACK_COMMAND:  kb
FOLLOWUP_NAME:  MachineOwner
MODULE_NAME: GenuineIntel
IMAGE_NAME:  GenuineIntel
DEBUG_FLR_IMAGE_TIMESTAMP:  0
IMAGE_VERSION: 
FAILURE_BUCKET_ID:  0x124_GenuineIntel_PCIEXPRESS
BUCKET_ID:  0x124_GenuineIntel_PCIEXPRESS
ANALYSIS_SOURCE:  KM
FAILURE_ID_HASH_STRING:  km:0x124_genuineintel_pciexpress
FAILURE_ID_HASH:  {0aebd40d-d4c8-456d-b299-4fede7e8bf0c}
Followup: MachineOwner ---------
6: kd> !errrec ffffe000e371d038 =============================================================================== Common Platform Error Record @ ffffe000e371d038 ------------------------------------------------------------------------------- Record Id     : 01cfce10254da6d6 Severity      : Fatal (1) Length        : 672 Creator       : Microsoft Notify Type   : PCI Express Error Timestamp     : 9/13/2014 1:02:14 (UTC) Flags         : 0x00000000
=============================================================================== Section 0     : PCI Express ------------------------------------------------------------------------------- Descriptor    @ ffffe000e371d0b8 Section       @ ffffe000e371d148 Offset        : 272 Length        : 208 Flags         : 0x00000001 Primary Severity      : Fatal
Port Type     : Root Port Version       : 1.1 Command/Status: 0x0010/0x0407 Device Id     :   VenId:DevId : 8086:2f08   Class code  : 030400   Function No : 0x00   Device No   : 0x03   Segment     : 0x0000   Primary Bus : 0x00   Second. Bus : 0x00   Slot        : 0x0000 Dev. Serial # : 0000000000000000 Express Capability Information @ ffffe000e371d17c   Device Caps : 00008001 Role-Based Error Reporting: 1   Device Ctl  : 0027 ur FE NF CE   Dev Status  : 0007 ur FE NF CE    Root Ctl   : 0008 fs nfs cs
AER Information @ ffffe000e371d1b8   Uncorrectable Error Status    : 00004020 ur ecrc mtlp rof uc ca CTO fcp ptlp SD dlp und   Uncorrectable Error Mask      : 00000000 ur ecrc mtlp rof uc ca cto fcp ptlp sd dlp und   Uncorrectable Error Severity  : 00062030 ur ecrc MTLP ROF uc ca cto FCP ptlp SD DLP und   Correctable Error Status      : 00000000 adv rtto rnro dllp tlp re   Correctable Error Mask        : 00002000 ADV rtto rnro dllp tlp re   Caps & Control                : 00000005 ecrcchken ecrcchkcap ecrcgenen ecrcgencap FEP   Header Log                    : 00000000 00000000 00000000 00000000   Root Error Command            : 00000000 fen nfen cen   Root Error Status             : 00000000 MSG# 00 fer nfer fuf mur ur mcr cer   Correctable Error Source ID   : 00,00,00   Correctable Error Source ID   : 00,00,00
=============================================================================== Section 1     : Processor Generic ------------------------------------------------------------------------------- Descriptor    @ ffffe000e371d100 Section       @ ffffe000e371d218 Offset        : 480 Length        : 192 Flags         : 0x00000000 Severity      : Informational
Proc. Type    : x86/x64 Instr. Set    : x64 CPU Version   : 0x00000000000306f2 Processor ID  : 0x0000000000000006

Error 124, I have to ask, what is your CPU clocked to?

Everything is completely stock.
 
bigmyke, I don't think they are exactly the same, but I do believe they are related. When I switched my video card slot to PCIE Gen 2 I stopped getting the error. The device IDs from both our error reports match. The symptoms aren't the same, but I would wager the root cause is nearly identical.

Same Issue here using two evga gtx 680's in sli, on an msi x99s sli plus mobo. I've tried everything. I dont know what to do. everything worked fine with existing hardware on my z77 sabertooth. 
 
A corrected hardware error has occurred.
Component: PCI Express Root Port
Error Source: Advanced Error Reporting (PCI Express)
Bus:Device:Function: 0x0:0x2:0x0
Vendor ID:Device ID: 0x8086:0x2F04
Class Code: 0x30400
The details view of this entry contains further information.

How did you install them?  Were the chipset drivers from EVGA installed before you attempted to install asus' chipset driver? i get a "computer does not meet the minimum requirements for installing the software" message when I try and install the drivers from Asus.

Corndogg18,
 
I called tech support a while ago about this and they said it is a bios bug and will be fixed in the next update. The cards are running PCIE 2.0. I have 2 480s and get the same issue (Bios says 1.0) but in windows it says running at 2.0. So cards are running at correct speeds; Evga just needs to fix and update bios to correct this.
 
 

Alrighty, here is your answer folks. I went to MSI, EVGA, Intel and Finally Nvidia to get to the bottom of the error. You will notice if you do a fresh install of windows or completely delete the nvidia drivers, the problem will go away. I confirmed with Intel support that the issue is definitely deriving from the PCIE bus, but rather than the bus itself it is whats plugged into the PCIE root. I came to this suspicion because I only get two of the following errors:
 
A corrected hardware error has occurred.
Component: PCI Express Root Port
Error Source: Advanced Error Reporting (PCI Express)
Bus:Device:Function: 0x0:0x2:0x0
Vendor ID:Device ID: 0x8086:0x2F04
Class Code: 0x30400
 
and 
 
A corrected hardware error has occurred.
Component: PCI Express Root Port
Error Source: Advanced Error Reporting (PCI Express)
Bus:Device:Function: 0x0:0x3:0x0
Vendor ID:Device ID: 0x8086:0x2F08
Class Code: 0x30400
 
both of the buses above are filled with nvidia cards but the 3rd slot
 
Bus:Device:Function: 0x0:0x1:0x0
Vendor ID:Device ID: 0x8086:0x2F02


is filled with my Soundblaster ZXR and of course.....no errors.
 
So I went to Nvidia, and low and behold it's a known issue. Something has changed with x99 and the way PCIE works, so nvidia is working on a new driver that will fix these WHEA errors. See the log below of my convo:
 
 Karthik: Hi, my name is Karthik. How may I help you?
 Matt Guy: hey how are you
 Karthik: I am fine thank you Matt, hope you are doing good too :)
 Matt Guy: Well sorta, I have an issue I hope you can help me out with
 Matt Guy: are you ready cause it might be a tough one
 Karthik: Sure, bring it on. I will try my best. 
 Matt Guy: Alrighty. So I bought the new x99 Sli plus motherboard from MSI as well as an i7 5930k. I have 2 EVGA gtx 680's in Sli that I transferred over from my old z77 intel 3770k build. For some reason as soon as I install the latest nvidia drivers, my computer starts producing the following error code about 25,000 times a day. 
 Matt Guy: A corrected hardware error has occurred.

Component: PCI Express Root Port
Error Source: Advanced Error Reporting (PCI Express)

Bus:Device:Function: 0x0:0x2:0x0
Vendor ID:Device ID: 0x8086:0x2F04
Class Code: 0x30400

 Matt Guy: under windows system event logs
 Karthik: I am checking..
 Karthik: This seems to be related to the kernel issue of the PCI express architecture (the error occurring randomly through the motherboard) 
 Matt Guy: Any idea on how to fix it? is it a hardware issue or something that a motherboard or Graphics card bios can update?
 Matt Guy: or do I need new nvidia drivers that are more compatible with X99 hardare?
 Matt Guy: hardware*
 Karthik: It does not seem to be a hardware issue but checking this for now, it seems the issue could fix with the next software update from our end. 
 Karthik: Yes it needs a newer driver update for the compatibility with the NVIDIA card & X99 hardware
 Matt Guy: alrighty thank you, yea the last thing I would want to do is send my motherboard back and wait for a new one to run into the same issue LOL
 Karthik: you are welcome Matt, hopefully everything should be fine & working. You may watch out for the new releases. 
 Karthik: Thanks :)
 Matt Guy: Are you 100% sure on this answer? Just because I am in contact with many people in the forums having this issue
 Matt Guy: if you are sure I can provide a response to all of these Nvidia customers and help out quite a few people who are in the dark
 Karthik: Yes I am sure, I do not see any other issue apart from this. The hardware is just fine & the problem is SLI specific only. You can wait for the newer updates & test this again. It should work.
 Matt Guy: ok, when I disable Sli though, I still get the errors :S
 Matt Guy: the cards are still plugged in physically together, but I disable Sli in the nvidia control panel, and I still get the error
 Matt Guy: sorry I'm not trying to be difficult, I just want to make sure that there is a fix coming, because im going to let quite a few people know that something is comig
 Matt Guy: coming*
 Karthik: Yes, there is no information on this further due to compatibility or other issues. You can keep updated that the future driver release should work for this issue Matt (specifically with x99 motherboards )
 Matt Guy: OK good stuff, I'm glad you guys are working on it! do you have any type of eta on a beta driver release date for this fix?
 Matt Guy: also is there something different in the way that x99 handles the PCIE bus that makes nvidia cards fail with it?
 Matt Guy: that was the last question i promise LOL ^^^
 Karthik: I am sorry, the driver releases are all scheduled by the development team. There is no specific ETA for now but you can check this from the GeForce.com site & the I have no access to QA details that test the way x99 SLI Plus PCIe is compatible or certified with the NVIDIA cards. So this will be internal data. 
 Matt Guy: but you do have knowledge on your end that this is a known compatibility issue at least?
 Karthik: Yes, I have seen issues reported on this model compatibility hence one of our updates should fix it. 
 Matt Guy: alrighty good stuff, that's all I needed to know, I shall wait for an update, thank you very much, you've been most helpful
 Karthik: you are welcome again & thanks for your time as well. 
 Matt Guy: is it ok if I copy and paste this to the EVGA and MSI forums for the people that are having this issue (there are other people with the same problem). they will be very happy that a fix is in the works
 Karthik: Sure you may post it, no problem. 
 Matt Guy: Thank you and have a great day
 Karthik: I would be happy, if this helps. 
 Karthik: Thanks, Goodbye! 
 
 Hope this helps all of you others that are having the issue. Cheers! hang in there and keep clearing your logs for now LOL

So do a full uninstall of the NVIDIA drivers, and reinstall them?