Good hypothesis about the audiobooks! However, they are regular mp3 files (I created them myself from cds at lower bitrates), so I don't believe that they have any bookmarking or chapter features (don't show up with any of my media players on the PC either). In addition, they pause and resume just fine if I do it manually ... so maybe it was some other glitch. I will keep a watch to see if there is any pattern.
In any case, I just thought of something - maybe I should create a profile called "DRIVING" with all notifications turned to "None" except the phone. Maybe this will prevent the player from stopping every time an email is received?