Hello Arturasz 
  
two years ago I had the same issue. I had to  exchange the clutch.I refurbish my Gangsteller because a little bit oil  was leaking (new custom gasket). Because the gearbox was removed I tock  the opportunity and had it refurbished too. 
The gearbox was filled  with new oil but the car (and the gears) had not been moved. I tried to  move the control shaft. It worked fine, but very precisely and tight.  The I started Getriebegrundeinstellung. It ran twice and stopped with  RTF 12 after the second 28th step. 
I started it again, same result.  Then a Friend of mine an I looked at the control shaft being driven by  the Gangsteller. All the measurement positions of the revers gear the  first gear the second, fourth and fifths had been reached. At the end  the Gangsteller moved but did not reach the neutral position. Then the  procedure started again automaticly for the second run. So the  Gangsteller was able to reach the neutral and the again the revers and  all other gears. After this second round I could read after step 28 the  RTF 12 error message. The solution for me was to announce every step  from 1 to 28 to my friend lying under the car watching the Gangsteller  and control shaft. After the I guess 4 measurement positions of the 5th  gear my frient helps the Gangsteller to reach the neutral position at  step 28.(Pushing gently with his finger to the screw that fastens the  control shaft to the Gangsteller.) This last movement of the Gangsteller  was too weak. 
With this the Grundeinstellung tooks only the first 28  steps and did not repeat them for a second time. The program finished  normally with the following steps (gas break and tiptronic switch  movements). 
I would guess there might be a software bug. The last  hydraulic valve impulse for leaving the 5th gear (to neutral) is too  short for a tight and new refurbished gearbox. 
After this  Grundeinstellung the A2 drives and switches normally until today (about  two years). Hope that might help and save some hours of trying and  watching the Grundeinstellung. Have a close lock at all the movements of  the control shaft. All the twisting to change the lane and the pulling  and pushing to select the even and odd gears. You should be familiar  with an ordinary manual gearbox. During the first 27 steps You can judge  weather the Gangsteller and gearbox work well. If so a little push at  the 28 step might help. 
Success  Cheers Carsten