I took the X3 in for its first oil change and asked them to reflash the software because of rough shifts. Turns out there is a bulletin on it. Bulletins aren't like recalls, they don't do the work unless someone complains about it. So if you feel like yours isn't shifting as smoothly as it should be, bring it up with your tech next time you are in for service.

What year X3? Do you have the SIB number?

There are 2...

One is for a customer complaint of any of these three things and it's SIB 24 08 07:

For E83 (X3) with http://www.bmwtis.net/tiscode/cgi-bin/new.gif 6L45R (GM6) automatic transmission produced from 8/2006 up to 10/2007
There is a delay in throttle response through the 1-2 upshift when accelerating from a stop.

There is a lack of power or hesitation when reapplying throttle, during either a 4-3 or 3-2 tip-in downshift. This may occur after slowing with a closed throttle.
Harsh downshifts when slowing on a roadway with a rising gradient (EGS is in a hill program).
The other is SIB 24 05 06 for X3s with M54 and GM5 trans:

The customer complains that the transmission will not upshift, usually after going up a slight incline, and stays in either 3rd or 4th gear too long.

I haven't seen anything like that for the 2005's, which is why we went that route. I've heard nothing but complaints on the 2006-up X transmissions.

Ours is a 2008, so it is within the first one. The car had rough downshifs when slowing and rough upshifts as well.