I had software issues with one of mine. They did a few updates but it never really cured the problems. One was 'lag' out of junctions which is a common problem I just learnt to live with and the other was that it was aggressive against the handbrake when waiting at junctions. The standard 'slush box' auto I had in the A4 previous to this was faultless for 90,000 miles. It wouldn't put me off having another if I needed an 'auto' though.
My mate had a total failure in his 8P A3 3.2 DSG. He reversed out of the driveway and the car lost all drive. It had to be abandoned at the side of the road and recovered by Audi.
However, to counter this lots of people have no issues at all. It's the luck of the draw. Luckily both examples above were in warranty so avoided an expensive repair bill. I wouldn't want to own one outside of the warranty period though.
I believe the CVT box is far more troublesome which is where the warnings probably come from. If the current S-Tronics were really problematic there'd be lots of press about it by now.