if you go into the BIOS, there is the option to disable the QControl of each fan, maybe you could try disable the CPU fan control by Qcontrol and let Fractal Design run by its own, will it work?
I have a similar situation - I'm using NZXT X61 AIO watercool. X61 have its own control software. The software try to maintain the fan speed while I see the Asus AIsuite try to overtake the speed control. This looks like not a really good condition if my system running in a long period. Does anyone else have a good solution?