I've got my iPhone and '06-325xi paired up. I've run into similar issues around it not pairing up again with the car, I think it occurs only in certain situations. It may be that the phone is inactivating the bluetooth radio if it doesn't find a discoverable item over the course of a certain amount of time, possibly to save battery? I dunno, but I noticed that it worked fine prior to me charging the phone overnight too. Yesterday after leaving work the phone and car paired up fine on start-up of the car. But last night I charged the phone and then this morning I had to re-pair the two.
Also, I've noticed that people tend to not hear me well over the iphone bluetooth also, I didn't have this problem with my prior Audiovox phone.