It could be the door motor that locks and unlocks your car.

I've got a factory alarm system on a 98 Accord EX-L and recently my drivers side door motor has gone out. The remote responds and locks/unlocks the passenger side door, but never the drivers side door. and when the car is completelty locked and armed it won't unlock the pass. side at all b/c in order to unlock pass. your drivers needs to be unlocked and since it can't... <- yeah i'm rambling