Yes I have had this problem along with a number of other people with the same engine. I'm not sure why the problem only effects some cars but you run the same tune on another "identical" car and it will behave normally and then on some other specific cars it misbehaves.
Here's a comparison dyno of 2 tunes showing the issue:
Attachment 30475
It's like it has a nmassive flat spot around 2,500rpm and then after 3,000rpm takes off.
All I can say is work with your tuner to get it resolved and if they can't get resolve the issue in a reasonable time to your satisfaction then get them to flash it back to stock and refund you any money paid.
I have heard of this issue on a couple of Tiguans as well as some Mk6 GTI which run the same motor.
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