In the process of upgrading the CPU, did you do a BIOS Reset on the mobo? Usually that involves removing a small disk battery and / or moving a jumper on pins (see your manual p. 36). I ask because you might have reset the CPU_FAN1 configuration.
Another possibility occurs to me. If you plugged the CPU cooler fan into the PUMP_FAN1 header instead of the CPU_FAN1 header, the PUMP header does no control, and always runs its device at full speed.