Yes, I see this too. I believe it is a crash of the iBooks app when switching from other apps (or using the button on the earplugs) after the app has been idle for a while (> 20 minutes?)
A workaround for me is to always launch the app, wait for it to load my books (takes 30+ seconds for me), wait for it to reopen the book I was last playing, then wait for it to start playing. The process is painful, maybe I have too many books/tracks (about 60 audiobooks right now).
If the app comes up right away, or the lock screen still shows the controls, I find that iBooks will start off in the right place. If the player is gone from the lock screen, and I try to press the button on the headphones, it will lose my place. But if I do the launch and wait procedure above, it will remember.
If you know you are going to stop listening, I've been able to force it to save the place by pressing HOME, then doubleclick HOME, then swipe the iBooks app up, (killing the app), then relaunch iBooks next time. It seems like it only saves the bookmarks on a clean exit. It would be helpful if it saved at least once a minute, or on a crash.
Hope that helps. Hope Apple is listening. --ed
