Your intake manifold could be malfunctioning. My flaps were not operating correctly(opening fully), even when tuned out. I'm pretty sure mine was no good before 80k(before tune). I'm at 150k now. Unplugged it about 15k and a trip to Colorado ago.
I got about 5mpg gain on the highway after unplugging it. I can get 50mpg pretty easy now, where I could hit 45mpg max before. I can get 45mpg with an 18 cu Skybox on top now with a tail wind.
I had no CEL and no other symptoms other than a random hard start/white smoke and problems with my methanol injection. I also had low mpg's, but I figured it was the tires/driving style/etc. But mileage jump has continued...Car also runs/sounds better.
I know of at least one person who checked ash load after unplugging it and found no noticeable increase. I see little harm unplugging it just for testing purposes. Just don't idle it for long periods and don't lug it. They are supposed to be fully open by 3k if I remember correctly. Without a tune you will get a CEL.
http://www.natef.org/natef/media/natefmedia/vw files/2-0-tdi-ssp.pdf
Page 12 - Intake Flap Motor v157
If you unplug it, flaps should default open.
Mine was actually making a lot of noise on shut down, as if it could not figure out where to stop. If you open hood, then shut off car and go to manifold and listen, you can hear it positioning itself. I am not sure how long it takes normally, but mine was definitely taking much longer than normal to get to it's desired position. That is what led me to unplug it, which it remains until Les gets new intake manifold sections minus the flaps