I had this same problem. It was really noticable and I took it to the dealership and told them they needed to update the flash for the transmission. I found this information on this website. They did flash the vehicle and it is less noticable but not completely gone. Here is the link that describes the same problem that I had. Hope this helps.
http://www.xoutpost.com/x5-e53-forum/...e-awesome.html
Tracy