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The following two images are from Calibre and the epub editor Sigil; the one from Sigil is its metadata editor. Notice how the tags in Calibre match the two dc:subject metadata lines in Sigil's metadata editor. So my guess is that the PocketBook is getting and setting its tags from the epub's dc:subject metadata. Deleting the tags in calibre apparently does not delete the tags from the epub's metadata; i.e., calibre has its own metadata; when you add the book to calibre it sets its tags from the epub's dc:subject metadata (just like the PocketBook is doing).
So I'm thinking that you need to delete those dc:subject metadata entries from the epubs. There are calibre plugins for modifying epubs and maybe one of them will fix the metadata for you.
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