The master key arms and disarms the alarm system. You seem to have fallen victim to one of those mysterious sets of circumstances which trips the alarm. The fact that you disabled it with the proper action (key in door) indicates that it's probably OK. As long as it doesn't get weird on you, as Larry said, you'll forget it's there. It's nice to have a dealer fix something w/o soaking you for something you don't really need. (alternator).. Stay with that one for future reference and maintainance.
2000 Dodge Grand Caravan SE