One thing to keep in mind, as part of their "Efficient Dynamics" program BMW does things a little differently with the charging system than most cars. They intentionally try to run the alternator as little as possible, the idea being that they then run it very hard while coasting or stopping. This saves gas - think of it as a very, very, very, very mild hybrid system. But I can see why short commutes can be a problem. Great theory, possibly not the best execution. There was a fascinating white paper on this floating around the forum a year or so back, but I can't find it now.
Note that this is also why there is the whole battery registration thing - the computer needs to know the state and what size/type the battery is so it doesn't go too far in that hard charging.
'11 328! Touring - Tasman on Chestnut, 6spd manual, factory upside-down "i" option