With an Audiobook losing its play position when you go back to it, it’s usually an iOS (the iPhone’s operating system) issue since bookmarks are handled by the OS. In our tests, bookmarking is maintained as expected to, although we've worked with another user recently that had a similar issue. In this other case, restoring the iPhone's iOS software got things going again, so perhaps you could give that a try. To do this, make sure everything's backed-up and then follow these steps, provided by Apple:
http://support.apple.com/kb/ht1414Keep us posted on how that goes!