James Mason :
It's a bit wierd, they should spin up.
You might have to check the BIOS to see if they see the CPU fan.
Does the fan actually spin when the system is working? if so it's probably fine, the heatsink alone is enough to protect your CPU in the BIOS.
Well, I tried something else in the meantime and it ended up with some different results. The Phanteks Enthoo Pro has this little hub at the back of the case with a couple of 3pin connectors which, I believe, is for the case fans.
Now what I did which (sort of) worked is, I put my CPU fan 4 pin connector (which was first in CPUFAN1) in the hub.
And the case fans connector (which I put in SYSFAN2 at first) in the CPUFAN1. Now, upon booting the system, the case fans and CPU cooler both spin.
The reason I said ''sort of worked'' is because although my CPU cooler spins upon booting the system, it stops spinning after the system is booted and never seems to spin, the case fans however, do always spin. Is this because the CPU Cooler is PWM controlled? Because that was my first thought, however, even under load it never really seems to spin either (under load I average about 72 degrees celcius in temps).
I also checked HWMonitor where the ''CPUFANIN'' is spinning, but this I believe are the numbers from the case fans spinning as those are in the CPUFAN1 slot.