Quote from alanack:
Thanks. For anyone who might experience this problem and come across these posts, the problem turned out to be Speedfan automatically resetting some things... I went to configure - advanced - selected the chip - and under PWM 1 mode and PWM 2 mode Speedfan had reset the value to SmartGuardian(whatever that means) - anyway, I reset these values to "computer controlled" and the fans got going again, everything is fine - it's still a bit of a mystery, though, as it will still occasionally reset these values...