Even newer update: Reinstalled Windows, K-lite codec pack, uninstalled K-lite codec pack, installed Sonic Studio, set front panel to AC97, and hey, no pop and crackle, it may have been a codec problem with the K-lite codec pack. (No I didn't reinstall Windows because of this, I was okay with how it was, but once I had the option of cleaning up the codecs, well... Not sure if the AC97 thing is important on a clean install, but I do not want to jinx it now).
Newer update: Uninstalled the Realtek Audio driver and SonicRadar, thought I could run Sonicstudio with the Windows drivers, but that did not work. However the snap, crackle pop issue persisted, so at least I have succesfully narrowed it down to a SonicStudio problem (Mind the Realtek drivers still have a problem with the front panel, which the Windows Update supplied drivers do not, as of 17. march 2018).
Update: With Audio_6.0.1.8273_20171225 got crazy crackling and popping even with the sane solution and the crazy pants options (Switched front panel from AC97 to HD though, and that helped ...some, very wtf...)
I have an IX Hero with the same problem (same sound card, same drivers)
What mostly works for me is this solution:
https://rog.asus.com/forum/showthread.php?47709-Sound-issue-(crackling)-with-Maximus-VII-HeroSwitching from HD Audio Front Panel to AC97 Front Panel.
Also do not run the volume up to 100, I do not go above 90. The Windows driver do not seem to have the issue, although you get snap crackle and pop there too if you run drives at 100% (i.e. defragging them).
If that does not work, you are down to the crazy pants stuff, disabling all other sound cards (like HDMIs from graphics cards), trying it out with antivirus disabled, turning the microphone down to 0, disabling the boost on it and then disabling it all together, disable the line in, the digital out and so on, everything but what you are using. Enter the Windows sound panel and in the communications options tell it to do nothing in the event of communications. In power options customize the power plan you are using, turn the PCI Express->Link State Power Management to: Off. Power the computer down, unplug the cables, let it rest 5 minutes, plug the cables back in, that kind of thing.
Maybe there are other crazy pants things to consider, I do not know.