My Trooper does this strange thing. When it is started the turn signals in front and brake lights in back all flash as if the alarm was going off, no horn though (thank God!). This continues for a few minutes of driving then they stop. I dont understand it but I do think it has to do with me using the power door locks somehow, could be wrong.
Any ideas?

 

Something sounds shorted.
Do you buy chance have a hitch with a Reese towing light adapter?

I know those always came into Toyota dealership causing problems. Designed for cars with red only brake lights. Cheap resistors inside them fail, and turn signals short into other systems through it. Like gauge/radio flash with blinkers or hazards with brake pedal...

If nothing aftermarket was added to wiring, then there's no easy guess starting point. Try to find an actual factory service manual, not just Haynes/Chiltons. They have way more accurate and clear wiring schmeatics in the factory one. Find any wires that tie into alarm, and follow them through the vehicle looking for broken wires, or bare wire touching other metal...