Actually I think I just might've, at least it worked perfectly for me so far, and I had the exact same problem.
It appears to be more of an issue with iTunes rather than iOS 5 to me, since once I tried using a program called "CopyTransManager" it worked perfectly with mp3 Audiobooks. That particular program (which basically does everything iTunes does) is even Freeware too.
You can download the entire suite here (though other apps are in trial mode):
http://www.copytrans.net/copytransmanager.php
What I did was delete my Audiobooks (in mp3 format) off of my iPod Touch 3rd gen, (though you could use trial version in suite to transfer back to computer) and then set them to music format in this prog, before resetting them back to Audiobook format. Once transferred onto iPod using this app, worked like a charm again. (playing and saving bookmarks, etc.)
I haven't tested it that much, but am quite happy so far being able to listen to Audiobooks in mp3 format the way I used to in older versions. So it does appear to be iTunes related to me.
Note: Just make sure you use latest version as older ones aren't compatible with iOS 5 and will report data corruption when there isn't any.