KB4100347 update is the one you need to uninstall. It breaks overclocking and other things on X99. It caused similar issues for me too on 6900K, I was trying many things in BIOS and nothing would make overclock actually apply, but as it turned out it was all because of this update. First time ever I had any issues with Windows Update. All of this Meltdown and Spectre cheap drama in media turned out to be way more damaging than Meltdown and Spectre itself, because issues caused by all of those "security updates" are countless while I haven't heard about a single confirmed example of Meltdown and Spectre affecting PC user. But it does affect everyone now, through security updates
Does it have similar effects on X299?