Yeah, like AZRAIN said try and take a picture so we can see what the flap is you are talking about then maybe we can help you. It's kind of hard to figure out what you are talking about based on your description. I don't have anything like that on my base model '96. Nolan also has some pictures of the underside of his 2WD 4runner, look at his website and see if anything on there looks like what you are talking about:

http://members.cox.net/nolanlh/4runner_suspension_tires.htm