Along with the beep, the light on the dash blinks out a code. The number of flashes indicate what the problem is (at least somewhat). The codes are listed in the alarm manual, and I think in the owner's manual. They are also posted in a couple of threads on the forum.
Typically, you will get one of two codes. One indicates that something isn't closed - the doors, the engine cover, or the access panels on the front (it's often this one if the covers aren't on just right). The other common code is usually about the motion sensor - the interior light has to be positioned in the down position and sometimes it gets "bumped" up (yes, the light circuit is tied into the motion sensor power).