*****If anyone is still under waranty, re-set your settings to stock, and take your car to the dealership*****
I had the same problem with a 07 GLI. I did regular DSG resets and it would help for a week or so, then right back to the same thing. It got to the point where I would just run it at stock settings to help minimize the jerking. As I neared the end of my waranty, I pushed the dealership to find the problem. When they were trouble shooting, VW told the dealership to drain the fluid. When they did, they found metal filings and replaced the tranny. Problem solved. I don't think the metal filings caused the problem, and I don't know if the problem caused the metal filings, but after the tranny was replaced the problem was solved.
In my opinion, it is not worth it to run the chip. If you want more power and you can't drive a stick, it would probably be cheaper to trade your car for a evo, than to have to buy a new tranny.
Now I have a different 07 GLI. It's stock, and doesn't have the jerk/hesitation when it shifts. However, when it shifts at about 3/4 throttle I can hear a faint "Pop" or "Woof" sound. I know it is the same spot my last car would hesitate or jerk.
I'm curious, anyone have this problem before the mech unit recall was done? Any change after?