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I formatted it again... Maybe it was something that was caused by Win7 (running XP at home, Win7 at work). I did check the metadata file. It was filled. I even deleted it completely and let Calibre create it again (again filled). I didn't get an error that it couldn't read or write. And it actually did update it when I added a book. It only lost all information when I reconnected again...
Weird...
Lesson learned: never trust Win7!
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