Ah, you did the battery/reset thing already. To be honest I know very little about those tiptronic but somehow I have a feeling it is management related. As in software.
Saying that; with all of that management & controls that the tiptronic runs onto, seriously, I can't think of any possible way that a gear could have been damaged. Unless originally faulty from factory then, unfortunate mate :/ Feel bad for you because that is not going to run cheap, removal inspection alone. That (@dealer) might runs you more than simply finding a second hand + swap at your local indy shop. Investigate that before (get quotes)
Raised by NewArt, that manual mode might be a little bit more forgiving - have you tried? If you are not having issues in m-mode, my advice is buy yourself one of those padle wheel (by RAID) and keep it on m-mode. Personally I can't recal when was the last time I've driven the car in auto mode mate, must have been in 2009 or something (when I got the wheel).