I have the same thing happening on my 2006 A6 Avant. My local mechanic says it's most likely the valve on the heater side of the AC control that is failing. It generally happens only when I am setting a temperature that requires a mix and the ambient outside temp is close my set point. We have not done anything yet waiting until the it does this all of the time (a complete failure of the valve).
I own a Audi A6 that will blow hot air out the side vents while the A/C is on. It also still blows cold air out the middle but the side vents get very hot. This does not happen all the time only every once in a while. I wanted to see if anyone knew what may cause this.