OK - I looked at this a little bit more.
The "across two installs" part is irrelevant
The part about the "books" being stored on a network share is irrelevant
The "file access" error seems to have been a one-off
But...
Progress is consistently erased for my "books" although they all have the option selected to remember it.
Here's what happens.
Start a "book," then stop at some point without listening to anything else after ("book" stays loaded in player). Close MB, open MB. Progress is erased on startup.
Start a "book," move on to some music, close MB. Open MB. Progress from the book is still there.
This happened consistently. I tried each scenario about 5 times. If I listen to something after the book, the progress gets kept the next time I open MB. If I close MB without unloading the book from Now Playing (I do stop playback), progress is erased when I start MB (I see the % Played actually go from a percentage to blank).
If it matters, I have "do nothing" selected for "On Startup."