How much volts does the Alarm System need? It is drawing too much volts off the battery and sharing it with the ignition system. If so, you need at least 12 volts - 14.2 volts to start the car off ignition. You're not getting that amount with the alarm system plugged in. By resetting it to default that may still not work. Find another way to power up the Alarm System.
Plus, I think the car works on two power up systems. It never has a not power on. Always powered on. So an auxilary battery at power off still will not work. Need more power to it yet.