With reference to that, it looks like a bit odd to me that the "PWM Mode 3" under "Advanced Tab" is still set to "Smart Fan IV" (and not "Manual" or "Software controlled").
If I set it to 'manual', it can only be controlled ... manually
There is no 'Software controlled' option.
You may also link the same case fan speed even to other temp sensors at the same time: for example the GPU temp, in order that the case fan will speed up either when CPU temp ramps up, or when GPU temp rises.
I've never actually used the CPU2 header (I use the CPU1 header); I just reported what others have said about it. Apparently both CPU1 and CPU2 speeds are controlled together (CPU1 is a 4-pin PWM-only header, and CPU2 is a 3-pin [PWM not voltage] header). Speedfan can't read the RPM of the CPU2 header (or control the speed of the CHA2 header) because those use a chip that Speedfan doesn't recognize (yet).
The only header on this board that is fully compatible with 3-pin fans and SpeedFan is CHA3. CPU1 and CHA1 are 4-pin PWM headers, CPU2 and CHA2 are 3-pin but not fully supported by SpeedFan. PWR is 3-pin but always 12V.
I've hooked up the case fan to CPU2, and it can be read and controlled (set to Smart Fan 4); it works great.
The fan on the heatsink is pinned to CHA3. It can be controlled manually from 0-100%, but when set automatically (Smart Fan 4), it is always 67%. (It's no big deal, because it's inaudible at that level.)
Anyway, I'm happy with this setup. The computer is sitting on the desk, and at idle, it's almost inaudible. When the CPU is stressed to 100% (@4.8GHz), noise level is acceptable, and temps never reach 80C.