I vaguely remember people mentioning having to download (or send, or push, whatever, as long as it's done through an Amazon service) a book from Amazon to 'unlock' page numbers, which makes no sense whatsoever to me, because it's not a feature tied to the registration process AFAICT, and as eschwartz said, it's a single measly file sent by Calibre during the "Send To Device" process...
What I can say is that the format changed a bit with the advent of KF8, but I can't remember how Calibre decides which format to send (and I'm the one who did the KF8 tweaks for that... >_<").
EDIT: Yep, I went with what I thought was the safe way at the time (i.e. sending the new format w/ KF8 files, and the old format w/ Mobi6 files, instead of checking the target device model to make the decision [which, while doable, is annoyingly complex and potentially not 100% accurate on every platform...]).
TL;DR: So that might explain it, and the trick might be to – if it doesn't work with KF8 files at first – try sending a Mobi6 one to 'unbreak' everything
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