I know this is a necro thread, but if anyone is still looking for a solution after all this, my problem was dirty power. I was plugged into a failing surge protector, and as soon as I replaced it, my latency was gone. Note, I also unplugged extraneous USB connectors from the motherboard while I had it unplugged, but as I was doing that I bumped the outlet and my monitor powered off from the protector. So I replaced it, powered up, and bam! After tearing my hair out for a week, running latencymon and replacing drivers, changing MSI registry keys, reinstalling windows, changing bios settings, audio settings, display and network settings, and whatever else, the crackling is totally gone. And to be clear, I had the same symptoms as other people on here, crackling under CPU load, high ISR and DCP counts for drivers, random but infrequent BSODs, so it definitely felt like I had a bad board after all that diagnosing, but nope!
So if none of these other solutions have been able to help, try another outlet (on a different circuit) or surge protector.