Water can easily sneak in under the sunroof when it is in the vent position. So guess this could be what is causing the smell if there is mold on top of the sunroof cover or even inside the roof itself.

I forgot the name of the stuff, but its like Ozone or Odium or something like that, but its what hospitals use to get rid of smells. Try spraying some of that in there? Or there is always Fabreeze?