Nope, that doesn't sound normal. It's basically the same problem you had initially only now it doesn't jerk the drivetrain as it did before I think. I don't know how long you had the mech issue before you took it in, but it's possible the problem going on a while took its toll on the trans. I'd push Audi to get the trans replaced if possible or extend it's warranty to far beyond the 2 year 24k miles they want to push for.
Also, when you talk to the regional rep, make sure you state to them that you didn't decline the warranty extension, you indicated that you still wanted to talk to a regional rep because the way the service advisor had positioned the warranty extension, they basically gave you an ultimatum. Take the warranty extension and pretend you don't have a problem or escalate the issue so that someone else can take a look into it.
Like I said before, I have a hard time believing that other S4's on the lot that aren't 2010-2011 with questionable mechs/trans make this same noise. I'll have to listen to mine, but I'm pretty sure I would have heard it by now if it was to have happened and I sometimes drop it into N when I'm waiting in line at drive-throughs when it takes forever to move up and get your food.
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