I've run into this as well on my X99 A-II occasionally. It seems to spike for me, but then go away, so it's a little baffling. I also have the 1070 Strix OC and only once did the lights get out of sync, so that hasn't been an issue. I like the ability to sync up lighting effects, but if it's going to constantly get into 8-10% CPU usage area, I don't think I can justify using it, especially since I'm using this PC for some heavy workloads.
Side note, I've noticed some bugginess with AI Suite 3, particularly when it made my GPU go haywire and I had to reset Windows to get things working again. I've learned not to touch the GPU section, which is probably just a dumb move on my part since GPU Tweak II is on my system as well (which also seems buggy at times).
Love the board, love the GPU, meh on software.