just curious, you mentioned 'main switch' on the side of the furnace. later you said sometimes when you turn it on by the 'main switch'..... in the second instance - are you referring to the same switch, or are you referring to your thermostat as the main switch. i was just wondering if you are turning it off and on at the furnace.
clicking of relays on the circuit board or even in a digital thermostat may be normal clicking of relays closing. the delay before the fan comes on also may be normal time delay designed into the thermostat.......this is to allow for a pre-chilling of the evaporator. there is usually a delay before the fan turns off as well.
if the fan does not shut off at all and you are indeed seeing a polarity error message, there could be a condition in the controls that needs looking into by a trained technician.