OK, new empty library folder, Tag Test
Sync one book. Has Tag set in calibre ("Fantasy"). Tag appears in justRead.
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1. remove all the tags in calibre and sync, does it display OK in justRead
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Removed tag in calibre. Now no tags on book in calibre. Sync shows a changed book. After sync...
Book in justRead has tag  !
in list of all tags there's only  
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2. add tag TEST in calibre and sync, does it display OK in justRead
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Tag TEST added in calibre, sync done, book in justRead has tag TEST (and tag   does not show in list of all tags - only the TEST tag)
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3. remove all the tags in calibre and sync, does it display OK in justRead
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tag   is back again.
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4. add just those tags you need in calibre and sync, does it display OK in justRead
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Just the Fantasy tag is back again.
NB I never manually added the tag   to this book in calibre. calibre must have read it from the metadata in the original AZW3 file or EPUB.
Could it be that when there are some tags set by calibre, you pick those up, but if no tags are set in calibre, your code goes looking for tags in the book file itself? (I'm not quite certain how the calibre sync stuff works).