I have a 2005 545i, I think you're talking about the same issue. I went to my dealership and they quoted me $700 for a programming fix since programming isn't covered under CPO warranty. I declined it and reported the issue to the NHTSA. The service director called me back and offered to cover it under a "goodwill" warranty since this is a known issue. The SIB below is for the 545 model.
The following software errors were corrected with the release of CIP 17.01(Target data Status E060-05-06-500).
Vehicles equipped with 6HP26 up to 4/05, customer complains of harsh downshift. Refer to SI B24 03 05.
Here is the SIB240305 bulletin:
Harsh 2-1 Downshift
E60 (545i); E63/64 645(Ci/Cic) with 6HP26 up to 04/05
Customer may complain of the following:
An excessively harsh 2-1 downshift when decelerating to a stop, or
Transmission "bangs" into gear when accelerating from a full or a "rolling" stop (vehicle did not come to a complete stop).
On a customer complaint basis only, reprogram/recode complete vehicle using SSS with CIP on-line update 17.01, or higher.
Transmission temperature must remain below 50 deg C and trans shifter must be placed in P position prior to the start of CIP programming.