Jeffy,

An electric heater is likely just an on or off thing - if it heats, it is still working, so it sounds like the controller is the issue. Maybe I'm misreading your post, but the heat should come on when the temperature is too low and the exhaust fan should be on when it's too high, so how can that work off of one thermostat?

Might the addition of the fan be overloading the thermostat?

What heater do you have?