Let's take it from the top:
1/ Delete the wonky books you have on right now (either via the UI, or over USB).
2/ If you deleted manually over USB, also remove the corresponding thumbnails in the system/thumbnails folder.
3/ If you manually deleted over USB, unplug & eject once before going any further, to let the Kindle catch up and update its internal catalog.
4/ Make sure your stuff was converted *without* the 'Enable sharing' in the MOBI output settings, and that the tag set to trigger the PDOC flag isn't part of the tags of your books. Reconvert if needed.
5/ Send books via Calibre's "Send To Device".
6/ Unplug & eject. You get covers & no PDOC banner. If you still get a PDOC banner, check 4/.