Hi Warheaven. Congrats on your first post and welcome.
Your setup is similar to mine, except my cooler is the Corsair H80. Also a double width radiator with push pull I brought over from the last build. It does work fine. However that one is a 3-pin and I think yours is a 4-pin PWM?
First thing I would do is follow the advice in
THIS FAQ RESPONSE. It indicates near the bottom of the solution that your PWM setup might be going through POST with the fan RPM's set too low, and so it thinks it's not there. It suggests changing your setup to establish a low RPM setting that the board will recognize. Since my cooler is seen by the board as constant RPM I don't have that problem, but yours might see it as 0 (zero) RPM on startup, even though as you indicated it does still work. Personally I wouldn't set a CPU cooler to 200 RPM min, I'd go higher. Even at 600 RPM your fans would still be basically silent. But setting it very low on a CPU cooler fan is chancy IMO in case your thermal paste isn't spread well and you have a few "hot spots".
Let us know how it goes.
Davemon50