These systems are fairly complex, with a computer module, sensors, actuators and all the wiring, there are so many possibilities. I would get the diagnostic trouble codes read out an diagnosed for starters. Also, have a shop check for any technical service bulletins that may be related to this issue.
I know this is an older post, but I just ran across it. Did you get this resolved? If not, try replacing the capacitor on the HVAC control board, as described at the site below. I had your exact same problem about 5 years ago, followed this procedure to the T, and have had no problems since. Cost me $11 at an electronics store. The dealer quoted me $1300 to replace the entire control unit. Good luck. http://www.macadamizer.com/bmwfix.html