Possibly one of the air doors in the heater/evaporator box is not operating for some reason. Not sure if they are actuated by vacuum motors or electric motors, but many of the newer cars use electrically actuated air doors. Sounds like something to be checked out by a qualified mechanic.
But before you jump the gun, try cycling all the controls for the heating and air conditioning, pausing for a moment or two between modes. Maybe something is just sticking a little.
