jetta tdi auto trans stuck? (bora uk)

I have a 2000 Jetta TDI. I recently lost my key and had to have a new one programmed at the local VW dealership. I had to have the car towed there which involved the tow truck driver having to pop the steering linkage in order to tow the car at all.

Once at the dealership the linkage was reset, and after the key was programmed, I was told that my after market radio had been removed due to a conflict with the diagnostic tool however it had not been reinstalled due to the mechanics unwillingness to accept "liability" should he mess it up during re-installation. After driving it home I noticed the car to be rather sluggish.

I found that when in Drive, it was actually in 3rd gear. Shifting to 3rd had no change, however shifting to 2nd and 1st gear did have an effect. Reverse still works. The car won't start in anything other than Park or Neutral (I know that's important via my Haynes manual) but I have no idea what could have started this. The trans was tip top before going to the dealership. Could that programming, or popping the linkage possibly started all of this?

Any help would be greatly appreciated.

Thanks,
Riebs