Two workarounds seem to be available:
1) Manually fudge the titles of your audiobooks to force the sort order you want in iBooks, as Breel21 suggests. This will make iBooks list things in your preferred order. But if you want them to actually play in sequence, you're SOL -- iBooks stops at the end and sits there, no auto-advance. So regardless the order they're listed in you'll have to open up the app and select the next one you want to start listening to. It's very annoying, and not at all good behavior when you listen to audiobooks mostly while driving.
2) To make playlists & ordering work properly, you have to force the files back into the Music app. You can do this in iTunes by changing the "File type" from Audiobook to Music. (Then make sure your sync is set up to load "music" from your audiobook playlist -- I went through some confusion when the files initially didn't want to transfer back to my phone.) As long as you've set it to remember your playback position, all should be well. You lose a little of the special audiobook functionality -- that handy 15 sec forward/back is gone when it's "music" -- but playlists work and it doesn't seem to lose its place anymore.
Neither option is perfect, but the 3rd party apps aren't that great either.