Sounds like a popular issue. I have the same sort of problem. As I see it, my car was originally designed to lock somewhere at rolling speeds, and then unlock when the car was put in park, or shut off. Then, you would get out of the car and click the remote lock button and all would be fine, with the Toyota security light blinking.
However, since I've owned the car, I've seen several issues. Here are some circumstances I've encountered:
I have gone for a drive and the car's locks have never locked after movement, and thus never unlocked upon parking.
I have been driving and heard the function (that locks the doors while rolling) click a few times, meaning it re-locked the doors that were already locked earlier. This one made me think it sounds most like a short.
I have had all of those functions work completley properly, gotten out of the car and hit the remote lock button, only for the blinky *Toyota Security* light to be armed, but the doors unlocked. After this, it was in a cycle of either being unarmed and locked, or armed and unlocked. Sigh. The only solution was to open the doors with the alarm armed (obviously setting the alarm off) and then re-do it all.. Interesting.
I have went to arm the alarm when getting out of my 'Runner and had the button on the keyless not work at all. That one has happened once, and at a friends house who's neighborhood I trusted a bit, so I left it unlocked. When I returned an hour or so later, the car was locked with the alarm on, so some timer feature must have activated or something.
Just a few strange occurances in my ownership of the 'Runner. I really don't think it's my ECU, but meh. I am livin with it allright, just get frustrated a few times a week.
