This is an old thread, but I just fixed the issue I was having. I (finally) went in and deleted all the internal data (via the Settings - System - Erase Internal Memory) and then resetting the folder structure (via the Settings - System - Reset Settings). That seemed to do the trick, and now my mp3 podcasts and audiobooks autoresume just as they should.
Of course, I did this all after backing up all my data.
And btw, here I am 7 months later and I'm still in love with my Pilot. The best $90 I've ever spent, and it shows no signs of slowing down.
- Brian Q.