OK, back to square one. Please confirm:
- The files that you're downloading via Whispernet are books, not periodicals created by Calibre's recipe system.
- The file is something you've imported to calibre, and perhaps converted, and has a .mobi extension.
- Prior to 0.6.46, these books ended up in the 'Personal Docs' section when you sent them via Whispernet.
- With 0.6.46, sending the book via Whispernet places the book in the general book section.
- If you connect your USB cable, delete the current copy on the Kindle, tag the book with [PDOC], and send that to the Kindle, the newly downloaded copy still ends up in Books, not Personal Docs.
Are those statements all true?