I had the same issue. I had a few things to fix, and finally found the culpret.
My rear hatch wire frayed and was disconnected, but that just made the module think the hatch was closed all the time.
My hood switch wires had been knawed through by a rodent and were exposed. If they somehow touched, this would have caused the alarm to go off.
But what was the real culpret (and probably yours too) was the glovebox. The glovebox switch doesn't get pushed in very far when the door is closed. Mine was only getting pushed in JUST enough to turn the light off. To check out if this is your problem, push down on the door while it is closed and latched.(do this at night or someplace dark. If you see the light come on inside, this is triggering the alarm. There is a screw that adjusts the depth of the door latch. Tighten this so that you can't trigger the light when the door is latched.
If this is not your problem and you still want to lock your doors without arming the alarm, there is a precedure.
Get out of car, open passenger door, use central lock button inside car, close passenger door. This will lock the doors w/out arming the alarm like locking the doors w/ the key does.
Good luck.