Check to make sure there is enough “exhaust” ventilation, including intake vents at the roof’s edge or in the overhang or undereave as well as exhaust vents high on the roof at or near the ridge. Possibly there isn't enough “exhaust” ventilation for the whole-house fan to run at the higher setting.

Call the manufacturer to find out the net free area of all the vents in your attic (intake vents and exhaust vents). Most net free areas are less than half the size of the vent. For example, a 12" x 12" gable vent's unobstructed airflow is 56 square inches even though the opening measures 144 inches. Calculate the unobstructed airflow of all the vents in your attic, whether it is a ridge vent, gable vents or undereave vents. If they equal the minimum requirements for the whole-house fan, the fan should run on high.