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More on metadata.calibre -- the code that updates it has not changed since the 0.7 betas. Unless you upgraded from 0.6, the permission denied error indicates that something else is going on.
Having an empty cache file will also cause calibre to show no books.
Try deleting the files, then start calibre in debug mode. When it sees that the file is not there, it will recreate it and repopulate it. Lets see what it finds, and whether some other exceptions are thrown.
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