Assuming this is on the 2006 Jetta.
The intake flapper works with the EGR valve to control air and EGR flow mixing.
So it throttles during operation.
Take a carefull look at the control unit again. Verify that all the little bent copper contact fingers are intact, clean and actually making contact.
Someone else recently posted that their intake flap motor was shorted, blowing their control power fuse. They had to unplug it until it could be replaced.
Power loss, No Boost?,water in fuel filter unlikely title, but this is the thread.