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When you crank it shut does the sunroof panel appear to be flush with the roof? If so you must have a torn or worn out seal.
For the motor itself, if it operates fine electrically to open, I would have to guess that you are correct that the switch must be bad.
Originally I was thinking you might have a cable problem, but that should be fine if you can operate it to close it manually in the trunk.
If it operates very stubbornly you might need to lube the tracks. Right now i would more concerned about the water leak.
Gilly
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