Update: ~13k miles. The dealer fixed one of the three rattles, two are still present.Mine does the same- only when cold (below freezing) and goes away next time it up shifts into 3'rd. Let us know what you find out. I am not sure if internal or external to transmission.
This car had the transmission re-programmed per the TSB. Is 4cyl SE.
It's summer here now and in the 90's and the thump hasn't been noticeable. the dealer only said "the transmission is performing as designed." They wouldn't acknowledge nor deny there was a noise. One potentially helpful guy at the service dept. told me to bring it in on a friday and leave it overnight for normal service and i could come by in the morning when it was cold and have a tech go with to hear it. When i tried that, i was told there were no techs working on weekends that could do that for me.
I've noticed a new thing the car does: steering wheel giggle. above 45 or 50 mph and above, if I "flip" the steering wheel a small amount really fast, the steering wheel will oscillate indefinitely! the car eventually vears to the left or right, but the steering wheel oscillates at about 5 Hz... and only the steering wheel. The car goes straight or slowly goes to the left or right. It's pretty wierd. I'll have to post on youtube sometime.