I always use send to kindle PC straight from my calibre library. I tag the books in calibre, make sure I have a cover etc, convert to mobi, then I open folder, right click and send to kindle.
They always sync perfectly fine for me, just like a book coming straight from the Amazon store.
I tested it just now just to make sure something didn't change and it worked Opened a doc on my Fire6 went forward in the book, went to my PW and hit sync to further read. Voila. Worked like a charm.
So yeah, its kind of puzzling if it doesn't work. Something else going on there.
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