2006 would have an electric motor driving the blend door, mixing of hot/cold air through the plenum controlled by the Temp control on the dash.
Typically if the blend door is having problems it will not change temps or "hunt" for a temperature, suddenly changing output air temperature without any movement of the temp control.
OP's situation sounds like the infamous vacuum reservoir is leaking, most likely the part itself although the somewhat fragile plastic plumbing tubing could be at fault too. Because the air flow is re-directed temporarily is one strong indication the vacuum system could be having problems.
On FTE there is an extensive thread about a relatively easy and inexpensive work-around--here's a link:
http://www.ford-trucks.com/forums/10...efrosters.html
Replacing the OEM vacuum reservoir is quite the chore, not something even this old DIY driveway mechanic would look forward to doing.
HTH