While Pentair automation controllers use a hard-wired air temperature sensor (located somewhere
outside of the controller's chassis, directly measuring air temp), the Intelliflo relies on a temperature sensor
inside its chassis, near the motor. It is measuring the temperature of the IntelliFlo's internal mechanics and electronics. The pump's "freeze protection" is primarily designed to protect the
pump, not your pool or its plumbing (as
@guinness points out). It only potentially protects your pool as a side effect of it warming
itself up. In fact, the pump's owner manual does not even call it "freeze protection." It refers to the feature as "Thermal Mode."
So while it's possible your IntelliFlo's temperature sensing is malfunctioning, it's just as possible that the internal temperature of your IntelliFlo never actually drops below the threshold that would engage its Thermal Mode. More importantly, the manual specifically warns against relying on the IntelliFlo's Thermal Mode to protect your pool or its plumbing. Jim's suggestion to run the pump 24/7 is the solution. Or perhaps just during the freezing hours, if you can reliably predict when those will occur (running 24/7 eliminates the guesswork about that).
Check it out (right from the IntelliFlo manual):
