sounds like the arm/disarm wire or mechanism inside the door isn't working. If you take apart your door cover, check out the key cylinder, there should be a green/white wire going to it. This wire is what turns off the factory alarm when you turn your key in the door. I don't think you can ever arm the alarm with the key, you have to use the transmitter or the lock switch on the door, then close the door. Either the wire in the door came off, or break in the wire somewhere, or the actual mechanism attached to the key cylinder in the door is bad..

13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
My webpage: http://eclipsed4evr.home.comcast.net
-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)