The factory code is kind of quirky in that area (might be a bug).
Normally, turning on the A/C will force the low speed fan to come on no matter what the coolant temp is. When a certain MPH is reached, it doesn't allow the A/C to force the fan on. Thats the only thing the MPH setting in the chip does.
If the A/C is off, and the coolant temp is above the fan ON temp setting, then the fan will stay on at all MPH's (unless you floor the gas, then it will shut off).
Paul, in your case, it could be that the coolant temp dropped enough to turn the fan off.