I've been an Audible subscriber since 2000, and this issue has come up quite a few times over the years. Apparently it's too difficult a problem for the engineers responsible. It doesn't seem that tough to me, though. It's the same as syncing anything else.
It was working OK before the 3.0 upgrade, and now it's not. It's really a pain in the butt when it happens. It doesn't seem to be related to any manual or automatic updating, too. Unfortunately the position is now lost if just connected to the Mac without even doing a sync.
My workaround until they fix it is to open the books I'm listening to and write down the chapter and minutes of where I am in the book BEFORE I connect up to my Mac, and reset them manually when I disconnect. It's time consuming, especially when listening to multiple sources.
There's really no reason why this isn't part of the test suite before a new release goes golden. Audible must be a low priority.