Just curious if your other Key fob was inside the car or in your wife's purse when she was inside the car?
I might be wrong..but here is a clue.
If you have comfort access key then you walk away from your car with key fob in ur pocket the car locks automatically and also the intruder/occupant-motion sensor activates, not sure if it will activate when engine is running. There is a chance that system thought some occupants inside the car when primary key fob is not in the perimeter...that might trip the alarm and auto-locking.
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