My 93 300SE does the same thing, but only on very long runs. If I stop and switch the car off and on, it will operate normally for a while but eventually I have to close the side vents to keep the hot air out. I had been having trouble with the door closer pump and I believe that pump also controls the operation of the vent flaps. Hopefully someone else can chime in here and offer some insight.

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2002 500SL(Black/Black)
1992 300SE(Black/Black)
1992 190E 2.3(White/Navy)
1999 VW Jetta TDI(Pearl Green)
1986 SAAB 900 Base 3 door(White)
1983 Porsche 911SC(Chiffon)
1977 VW Scirocco(DiamondSilver)