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The handling of cover thumbnails in the library view varies based on the type of e-book. If it is considered to be purchased or borrowed from Amazon (CDEType=EBOK in its metadata) then the thumbnail folder mentioned by tomsem is used to obtain the cover image. If it is a personal document (CDEType=PDOC) then the thumbnail is extracted from the cover image inside the book if one is present. Otherwise a generic cover thumbnail is used.
If you use Kindle Create to produce a KPF and convert that to a KFX personal document using KFX Output that workflow will produce a cover but it has other issues as you have found.
If you use send-to-kindle to convert a PDF to a KFX personal document it will not contain a cover image so the generic cover thumbnail will be shown. That differs from reflowable personal documents produced from an EPUB which will contain a cover when send-to-kindle is used.
The KFX Output plugin can update an existing cover but cannot add a cover to a book that does not already contain one so it will not help in this case.
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