It's a very common complaint. There are a whole bunch of threads in this forum about it (mostly started around July 1, when the update trashed things for everybody). A number of different workarounds and alternative apps are recommended by different people -- take a look and see if any of them help.
For me, the solution that has been working is to reassign the audiobooks (via the Get Info tool in iTunes) to have the media type "Music" rather than "Audiobook". This lets them sync back into the Music app, which plays them properly and usually remembers its place, plus it restores my ordered playlists and auto-advance when I finish a book -- neither of which are available in iBooks. You do lose some functionality in Music, inc. the 15 sec jump forward/back and variable playback speed, so it won't help if you need those.
iOS 9 will be out very soon, though, so we'll know soon what it fixes and breaks.