On my 97 SL320, ( which uses a later system that may or may not be similar to yours. ) the alarm would not always deactivate when I unlocked the door with a key. I ended up unplugging the RCL module ( Remote Control Lock ) to prevent it from sending a signal to the ATA module ( Anti Theft Alarm ) that one of the doors was opened. The RCL is tied to the IR remote key code so you can't just swap modules from car to car.

On the SL the, the RCL and ATA are in the right side of the trunk, near the fuel fill tube.