sorry if im misreading this, but if you are using a stock clutch the ecu has nothing to do with it. The fan clutch i believe is based on how fast it's spinning and the clutch engages when the fan is basically useless because air would be cooling it a lot better it shuts off. I wouldn't really worry about it too much it's not really hurting anything (i know this because my clutch is out so it's always spinning).
