Sounds like we have very similar problems... but mine started last night at about 1 am (ugh).
Same as you, I have a 3.2L '99 ES.
I can rule out stray frequencies, because it's happened in 3 different locations, and I can rule out my remote's transmitter because in all 3 instances I was too far away for that. Thanks to this thread, I can rule out the idea of a faulty motion sensor.
Any other ideas? Today when I got home from work, I went around and opened and "forcefully closed" all the doors and the trunk... but would that help determine if it's a faulty door/trunk trigger?
I'd rather not go aftermarket quite yet, so I really need to figure out what's causing this.