One of the theories for the noise is that it is a big door to an underground cavern, which Locke and the other dude found in the last episode (the metallic ground at the end). I noticed that when it started to rain, the trees started to shake and Clare said "There it is again." This might have been the door closing when it rained.

Matthew

It was that flying object in the pilot than landed in the landing bay. The doors swung open for it to land. :D

i'm confused....