Seems like you have the infamous Blend Door Actuator gone bad. This cars have an electric motor (Blend Door Actuator) that controls the mix between Cold and Hot air flow from the HVAC.
This cheap part is made with plastic gears that strip off with use, after it gets damaged the electric motor keeps turning, trying to get the Blend Door in the position selected by the driver (wether Hot or Cold) but cannot achieved due to the broken gears. that's the flapping noise you keep hearing!
Here is a search I did in this forum for the Blend Door Actuator
http://www.automotiveforums.com/vbul...archid=2262048
Read thru it for tips and procedures to replace it aswell as where to get the part cheaper than the dealer.