I have a 2001 4runner with the moonroof (or sunroof if you call it that). The moonroof opens automatically about 20 seconds after i start the 4runner, it takes me about 15 min of trying to close it with the button before it starts to close. For now I have disconnected the moonroof motor from the relay control box which is all located above the rear view mirror, so the relay still gets power but the motor does not. I can still here the relay switching on and off as I am driving. I don't know what would cause it to do that.

Does anyone have any idea what is going on?

Here is a picture of the relay assembly for reference:

 

http://www.ncttora.com/fsm/1996/SIL/...emci/041mr.pdf

Here is the wiring diagram. I can only see one possibility: a defective switch module. Nothing outside the box would cause what you have, as far as I can see.