I'm no expert at this kind of thing and haven't tweaked a computer in more than a year, but past experience tells me this is an issue of a pre-programmed behaviour, something like a Smart Fan function of some sort.
On an old Asus Mobo (sometime around 2008) I had a function in the BIOS called Cool&Quiet, which basically monitors the fans automatically (made the computer super quiet on anything except high-end gaming).
Now what I remember from that BIOS, is that the fan speed page and the the setting to put Cool&Quiet were on different pages, my point here is that since you also have an ASUS mobo it might be similar and you might have missed it. The thing about this function is that it disables all outer control of the fans; such as speed and voltage, in my case I used SpeedFan and was unable to control when it was on.
The question here is, what made such a functionality to be activated on its own. Well, it might be through some recent hardware/software update.
Suggestions:
1) Check forums of the Corsair Link and AI Suite 3 for similar issues.
2) Check every page in the BIOS for a possible similar functionality as the one mentioned above. If found, see if it's on and you know that it wasn't active before, then deactivate it.
Again, this is a modest answer to think about till a real expert shows up
GL with the new rig and Happy New Year!