Anti-theft System

I got a Camry 97 LE V6. A few days ago, my battery went dead and I jump started the car. Now everything works fine but the anti-theft system, which seems to be off. I remember that while I was trying to figure out what's wrong with the car, before given the jump-start, the system was still working as I set off the alarm a few times. I could stop it only by turning the key to ON position. The power door locks which work on the same remote control command are cuirrently fine. Does anyone have any clues regarding this? Thanks in advance. gl