There's an extended header (a few more fields needed, IIRC) needed for KF8 files. Calibre should be using it when processing KF8 files, though.
I'll take a look.
@Doitsu: Which FW version are you running, and has your device ever shown 'page numbers' since the last factory reset? (be it in an M7 or KF8 file).
IIRC, there's a weird quirk when it sometime doesn't like 'custom' APNX files until
something happens (AFAICT, either getting a proper KF8+page book OTA, or opening an M7 one).
Because Calibre's APNX work for me, and KindleUnpack appears to be doing the right thing in regards to the extended header for KF8 APNX.
I'm not sure I have a properly setup ePub book on hand to try it from scratch, and I'm a bit short on time until next week, but if someone has a dummy reduced testcase that I can try, I'd be happy to

. [Barring that, I'll try with the files Doitsu generated].