I've had grinding/rattling/shaking in my TI sedan getting steadily worse since new (June-12). I had the update last spring. Given the many posts here on this issues it's obvious that the shifting mechanism in these cars if flawed.
I brought it to my dealer last week to address the issues. Though the minimal grinding occurred (wouldn't you know it - normally it was a lot) when I took a drive with the tech, he knew exactly what I was describing (probably from other customers as well) and recommended my clutch assembly be replaced. They replaced it under warranty this week and so far the car drives better than it ever did with quiet smooth shifts. I'll report again after more milage.
I'm very happy with my dealer for supporting me on this with no begging required on my part