Welcome to the ROG forum.
Have you tried using the Shutdown Effect in Armoury Crate? At the top left of Armoury Crate, click Device then click your motherboard.
Click the picture to make it bigger.
This must be normal as mine does the same thing, it does the rainbow effect when booting up, once booted into windows it sets my color.
Since it works the same for me, this must be how the new version of Armoury Crate works.
I wouldn't sweat it if all is normal once booted into windows.