I figured I'd revive this thread.
I did have the update done. I figured if there were any issues that's the first thing the dealer would want to do anyway. I've put maybe another 1000 miles on it and the shift from 2-3 is still a jolt. Well I should clarify. It's a rough shift when between 1500-5500 rpm. I'm almost positive that the dealer did the proper learn procedure because there were 14 more miles on it when I picked it up from them.
I saw mention of a star case about this issue somewhere. Does anyone know anything specific about that? I'd like to have as much info as possible when I schedule to take it in again. That won't be until late March as my schedule won't allow for any sooner.