This does sound confusing. Did you notice this from inside the car? Does the car run normally other than this? Maybe something to do with the intake manifold or egr, my swirl flaps in the intake manifold were coked up bad and so was the egr. What about the MAF sensor? I'm no expert but trying to think of some possible causes, did you need a remap after blanking the egr?
i took the whole intake off the turbo and turned the engine off and the flutter still occured, i then attached it all back together, removed the intercooler hose from the chargepipe, turned the car off and the flutter was gone, i then turned the car off and quickly put my hand infront of the loose intercooler hose and a big shot of air hit my hand, so something is causing air to come from the engine, through the intercooler and into the turbo causing it to flutter.
