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You don't mention the book format used or how the books are exported from calibre and added to calibre. All three of these things can cause loss of metadata, if you are not careful.
Not all ebook formats support all metadata. Epub supports the most. Mobi doesn't support embedded series information. And so on...
One easy way to ensure that all metadata is included is to use the save to disk feature, and also specify that the OPF-file should be included. The OPF-file contains a copy of the metadata as it would have been if the format had been epub. Also make sure that when adding the book that calibre read metadata from the contents of the book, and not from the filename.
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