This definitely appears to be a bug in iBooks 3.1. I just submitted this to Apple feedback:
When I view a PDF in Safari, then open it in iBooks, it's supposed to sync back to iTunes. It just doesn't work. From your own website:
"When you use iBooks to open a PDF, iBooks will automatically save a copy of the PDF to your iBooks PDF shelf. These PDFs will also sync back to your iTunes Book library the next time you sync your device with iTunes."
It was VERY difficut, but I finally did it!
First I was annoyed because I couldn't get the PDFs to show in my iTunes Library. As near as I can tell, performing a backup of my iPad did that. In the past 'Transfer Purchases' did the job.
What nearly drove me bonkers was getting the content of my iBooks Library to sync to the device. There was just no way to do it. Not my PDFs and not even the purchased books! I tried to get the Library on the left and my iPad on the right so I could drag and drop. NOPE.
I played around a while and finally got both to show on the screen so I could drag and drop. STUPID
What I think worked for me: I started in Music Library and clicked on the +Add to icon on the top right. This pulled up my iPad for drag and drop. Then I switched the button on the top left from 'music' to 'books'. Finally I could remove or add my content to iBooks.
It worked perfectly before, why did they change it!
The music App makes me drag and drop, which I never had to do before. All I had to do was check or uncheck songs in a playlist and sync the playlist.
Apps works fine, no complaints.
Podcasts, another fine mess...
I noticed Video was fixed when I went back in.
Oh, the kicker, my iTunes is not responding today.