Hi Ronan. it should work with either kts or vag-com, I did one, and it would not start after 15 seconds as it should, So I did the procedure using vag-com, and then left if for half an hour before I tried to start it, It fired up first time. ??? ( don't know why, should it say 15 minmutes instead of 15 seconds ). ?? I have also programmed key's using KTS and it worked fine, (on a golf). have you now tried reading the fault codes to see what it is logging with the new ecu. ??