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Did the tech who did the CD player have the HVAC controls out of the car? If so you may have a mis-routed vacuum line. The other possibility is a pinched vacuum line. A failed vacuum controler seems unlikely in a 2000 SE, but it is possible. Could the tech have left something disconnected?
You may want to go to the local library and look up the vacuum hose routing, hose colors, and location of the vacuum actuators and "doors" for your heat and A/C system. Then determine if everything is connected properly.
Then start looking for a pinched or punctured vacuum line to the actuator that controls the vent/defrost door.
The color codes for the vacuum hoses should be (but I am not sure for your model year) defrost door - yellow, panel/floor door blue, source vacuum -black, air inlet door - white, panel/floor door red.
Also check the electrical connections to the EATC if you have it, or the manual system if that is what is in your car.
If this started to happen just after you had the CD installed, why not have the CD installer look at it? Did they screw something up? If so, let them fix it.
Just some thoughts.