I can't figure it out either, it seems to be hit and miss as far as what causes it. It can happen with a random file, or (more often), if I have to replace a specific book many times after re-edits.
I haven't tried waiting it out, I check and see if the options to show the percentage read is displayed under "Sleep, Light and power". If it's not, I reboot, if it is I relax.
Next time, I may try waiting and seeing if it fixes itself. I didn't try removing the file, though. Hmm.
Thanks for your reply!!!!