Upon further testing...
I noticed my MB (case) lights weren't on when I booted, and my mouse had the wrong effects also...
I opened Armoury to put the mouse lights how I want them, and when it opened, my case lights decided to flicker, and turn on - (not how I have them, some weird red<>white pulsing/fading thing)
I also have G.skill TridentZ RGB RAM, which I have un-synced in AURA normally (so they do their default rainbow thing) - but these were also 'enabled' and showing RED, along with my GPU....
after setting Armoury, I opened Aura, and set them back how I would like them, and they (seem) to work fine... (Unless I choose a colour OTHER THAN white) - then they fade between white, and the selected colour constantly...
i'll try get a video next time my case boots up without it's lights on, and video the whole process...