Forced Hot Air System?

I just moved into a towne house three levels 2200 sqft with two heat zones main floor and second floor my master bedroom is on third floor and is controled by second floor heat zone. The system is run off of propane and the towne house is brand new us being the first occupants but is three years old. My question is there is more than what I would consider as a draft almost like a blower is maybe turning but not on and cold air comes from out of the ducts until the furnace starts but makes for a very cold room like to keep it a 60 during the day and 68 at night. Is it possible there is an air intake flap somewhere in the system that may not be closing all the way allowing for the cold air to circulate through out the house.