Here's a wierd one...The only way I can arm my stock alarm is to lock the passenger side door then open and close the hatch. As soon as the hatch closes the system begins to arm. The position of the drivers door lock is irrelevant. I cannot arm the system in any other way. Also, opening and closing the hatch after the system is armed does not disarm or set off the alarm..only the doors set it off or disarm it... both doors DO disarm the alarm using the key. I'm a little confused here...

 

i'm going to hazard a guess that the unit is faulty, although one of the switches may be able to do it. have you looked in the FSM for your car and done any of the quick tests listed in there for the stock alarm system?