Might be resurrecting an old thread, but I'm experiencing the exact same thing with a Maximus X Hero.
When fans are set to PWM in the BIOS, there's random flickering and blinking on fan leds, which makes it really annoying. Transitions don't work fluidly either, because of the random blinking.
Change the headers to DC in the BIOS, and then lightning works wonders. A real pain, since switching headers to DC mode turns my PC into a plane about to take off =(
So I have to chose between high noise levels, or annoying lightning.
Any ideas? =(
Fans are connected to CPU_FAN, CPU_OPT and CHA1_FAN btw.
Oh, and probably worth mentioning, I think there might be something weird with PWM signals, since I had one of the controller channels connected to my GPU (just a regular PWM header, since one of the rads is there for GPU purposes) and that had the exact same effect.
At the beginning I blamed the GPU header for whatever reason, and moved on using a different approach, but seeing this makes me wonder, why do I get distorted lightning whenever I input a PWM signal to the TT Sync controller, from whatever source, be it MoBo or GPU?
Thanks in advance!