I have the same problem with my Maximus XI Code. I changed over to Amoury Crate, updated all the software within the app, then all of a sudden my leds stopped working. Found out the RGB header stopped working, so i switched over to an unused RGB header. Now I have 1 dead RGB header. This never happened when using the Aura Sync app.
It feels like one of the Armoury Crate updates fried my RGB header. Thanks Armoury Crate....