That's weird man, especially when the other fob works fine. Can't think of anything to 'reset' inside the car. Must be some key combination on the fob itself to 'reset' it, or somehow you messed it up during the battery change, but how?
The trunk could be locked from your glove box, so check that first.
Did you try contacting a knowledgeable SA at your dealer? You could also send a PM to BMWMD here and I'm sure he'd find out for you. Good luck, and keep us posted.