I've been having something similar to what previously described... just adding what happens to my kobo.
With a sideloaded kepub (and it looks like it's only this book, BUT i'd been reading it for a while and it wasn't doing it from the start) via Calibre with the extended plugin, I stop reading on ch5, go to home, and the % is 0 and it reopens at the beginning. I then go to ch5 via TOC. If I put a bookmark on ch5 and go out again the % is still 0. It shows there's a bookmark but when I open it it tells me there is no bookmark and again it opens the book at the beginning.
I've tried first switching on/off and then a factory reset, this one book is still doing it (and it was working fine before... before I went 2.8.1 but even the first few days of 2.8.1 !) while another one I tried is not. Mah.
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