Not sure if it's the same problem with audio files, but bookmark position is lost after a hard reset of the device (battery pull or a hard failure). After the device is rebooted (even while not listening to podtrapper), the bookmarked position seems to be accurate. However, when I hit play, it starts to play from the begining. I think similar problems have been posted in the past. Have you been able to make any progress on this? (maybe by saving the bookmarks to the download folder?)
thanks,
Ed