I have had the same problem on my 05 X5 4.4 since I bought it 3 years ago with 65k mls. I noticed on the service records that the original owner had taken the car to the dealer twice for the same problem while it was still under warranty, but every time he has been told that there was nothing wrong, and no fault in the computer!!
The car is now close to 100k mls and I am planning to do a transmission oil and filter service on it. Will report if it help with the issue.