I normally use Calibre Companion as my Android library manager and just use Pocketbook (or Mantano) for the actual reading. Nevertheless I just opened up the Pocketbook 'All Books' page in both grid and list views. In each view every thumbnail is exactly the same size, no matter what the actual cover dimensions are.
Is it possible that Pocketbook is 'remembering' your old cover thumbnail in its cache? In which case try deleting the book from the device using Pocketbook. Then resend the book with its newly edited cover page. I don't know whether this would guarantee that Pocketbook will re-create a new thumbnail, but it's worth a try.
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