I had battery issues with my 2006 X3. My battery died, so I replaced it. Only to have it dead again in 3-4 weeks.
After research, I found the bluetooth module is a problem with some newer phones. I dont know the details, but I did notice my phone would show a bluetooth connection when I was in the house, even though I was not aware of any bluetooth device. I didnt think anything of it as the phone worked fine. Apparently the X3 is continuing to look for and lock onto my phone when it is off and this 'searching' kills the battery. It has something to do with an approved list of phones, of which my new blackberry was not on it and most new phones are not.
I unplugged the bluetooth module completely (in rear storage area. Left side of rear hatch area opens to show the bluetooth module (silver finned box) of which you can unplug. I was not certain if just unpairing would solve it, so I just unplugged it. I actually removed it completely.
Zero issues since and that was 8 months ago.
2007 550i Sport - White - Tan