You might want to check that the nuts on the crossbars are tight. Can you shake either the crossbars or the rails - does anything feel loose?
Sounds can travel strange paths in a car and mask the real source. I think there was another thread a while back where someone posted the same problem, only to find it was the well-known rear seat rattle on the passenger side. There are also a lot of moving parts on the moonroof, so that's another thing to check.