Is it an aftermarket alarm system? I know Alpine makes a few security systems, but quite rare, at least from what I've seen out there. If this is the case, it sounds like the aftermarket system is doing its job correctly by unlocking the doors, but the factory Subaru system is still causing the vehicle trigger. In this case, you'd need to unplug the factory security brain and just use your aftermarket system. It's located under the console by the ebrake. Be sure the car isn't immobilized before unplugging it.
"We live for a good time, not a long time."
RIP Colin McRae