+1 on the leak possibility. Tom and I found water under the passenger side carpet when we (okay 90% Tom) were installing the Nerf bars. Turns out that the glass installer who replaced my cracked windshield two weeks earlier hadn't done such a great job resealing the glass. No big deal though, a I think I paid $2 for a tube of window glue @ Auto Zone and fixed it myself in 15 minutes.
May not be your problem, but wouldn't hurt to check the rubber seal to make sure it isn't loose anywhere.