Awhile back I was having crackling/popping noises while watching movies, music aswell as poor fps in gaming with my EVGA Z87 FTW mobo setup.  I did everything GPU and Motherboard technical support suggested (driver wipe/reinstall and even after upgrading to Windows 10 from Win7 problems still persisted, even rma'd GPU and still same issue, tried different PSU..etc...) and nothing worked.  I ended up RMA'ing Motherboard and still had the same issues.  Finally after I was waiting on my 3rd RMA on my EVGA motherboard (because I had another issue with the replaced motherboard unrelated to the main issue).  While I waited for the cross-shipment to arrive I continued to troubleshoot and found out that setting the pci-e setting to GEN2 or GEN1 in the bios I no longer had the noise and poor performance issues.  When I set it back to Gen3 problems returned.  Anyway, aside from this, I also have another PC setup with a EVGA Z97 Classified mobo that I purchased back in late May of 2015.  Today, I booted up my Z97 PC and the all too familiar problem occured.  Did multiple reboots, tested music, game and there was the dreaded crackling popping noises but fortunately no performance degredation.  Went into the BIOS and manually set to GEN2 and all was fine after multiple reboots and tests but I will not rest with knowing my GPU 3.0 is running at 2.0.  Currently we setup an RMA but I really feel we need BIOS update to resolve this issue.  If anyone of you encounter the same issues it could likely be the PCI-E Gen version settings. 

AKToronto
These generally sound like audio issues to me that aren't specifically related to the mobo... There are many things that could affect your audio set up.. This includes the location of your amp, subwoofer and all the cables that run audio as well as power.... Often its best to keep the audio cables and audio devices away from power cables and power sources. Ive had audio issues before and rather than trying to change things up in the bios it was more about positioning the audio equipment and keeping things away from power bars, etc, etc. The fact that you are experiencing the same issue with different motherboards does seem to suggest its not a mobo problem.

I am currently using the GPU HDMI audio(tested multiple HDMI cables and on different displays and audio system same result).  This problem occurred even with my other PC setup with a EVGA z87 FTW which was eventually replaced with a z87 Classified and all is normal ATM.  I am currently uploading a 10 minute video on Youtube of me selecting GEN3, GEN2 and GEN1 to show that my problem only occurs when GEN3 is selected as I do multiple restarts and launch benchmark or youtube videos so you can hear the cracking and popping noises when set to GEN3 3.0.

Do you have the nvidia hd audio driver installed? If so, uninstall it and retest the system.

Seems really weird.  Assuming you've tried different nvidia drivers.
 
1) What bios are you on, have you tried different ones
2) Are you using the intel gpu or have you tried disabling it, possibly with the integrated sound also disabled
3) Have you tried putting the graphics card in a different slot

Can anyone try setting GEN3 in your Bios.  I am curious to see if anyone else would also experience this noise issue aswell. 

Looks like it's definitely a hardware problem. 
 
Time to test the card in another system to see if the issue follows the card.

Playboyer, could you please provide some additional information for us to help troubleshoot this?
 
- Does this only happen over HDMI?
- Is your HDMI going into a receiver?
- Have you tried different HDMI inputs on the TV/monitor/receiver?
- Have you tried different speakers or a headset?
- Have you tried different PCIe slots?
 
 
Get me that info, and I'll pass it on to our product team for further evaluation.

And you don't get the crackling in Auto, correct? Can you try setting it to Auto, then boot up and check with GPUz to see if the board is running Gen3?  You'll need to use the renderer in GPUz to get the card to run at full speed, or it will clock down to a lower gen at idle. You can also check the Nvidia Control Panel as it will tell you what Gen the PCIe slot is running in the System Information found on the bottom left corner of NCP. 

I'm sorry, but unfortunately Youtube and other video sites are blocked by our firewall so we cannot view videos. Could you post a screenshot or just let me know the results?

Thanks for talking with me about the issue. I'm glad everything is working properly on Auto, but I'll pass on the info to the product team to see if we can replicate the issue forcing Gen 3 just to be sure.

I have had the same problem on z97 classified and I found the my OC CPU was the problem, When I took off the overclock all my problems went away. I just don't know enough about overclocking to do it right I guess. CPU 4790k was 4.5Ghz now stock. 

Ok I also had to unistall the onboard audio software not the drivers just the software also go into sound properties and disable all room correction/ enhancements too. See if that doesn't clean it all up,