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Sounds like your blend doors. I had a similar problem with my '06 only it was not a L/R thing. If under warranty, take it to your dealer to get the unit replaced.
Not sure exactly where the blend box is at.
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2006 F-150 SCREW 4x4, 20" P275/60 Goodyear Wrangler Silent Armors
Bedlocker, Line-X, Powergate, Rousch CAI
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