When you had your winter tires fitted, did you turn the suspension into the "change tire/jack mode" mode? It is very easily accomplished by pushing at the same time the suspension lift and suspension hardness button for a few secs. Then a warning message appears on the dashboard control panel and voila, done.
To switch this mode off, you just have to push both buttons at the same time again and the warning message disappears.
I guess that what it might have happened to your Phaeton was that if you did not turn the jack mode on, the suspension extended fully and when it went back to the ground it lost the rear height settings. So try to turn on the jack mode, wait for a little while, turn it off and see how it reacts.
I hope it helps and keep us updated anyway!