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If your books are in the MOBI format, calibre cannot update them. The MOBI format is old and flawed and does not support the cover metatdata type.
You can reconvert a MOBI, and calibre will use its own cover metadata prepended to the MOBI, or convert to AZW3, which is a newer version of MOBI that supports cover metadata and will update in the future.
Your profile says you have a Kindle Touch, which supports AZW3 -- I would suggest using that. You may have to configure calibre to send AZW3 first (see screenshot).
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