iTunes and iBooks delinked

[sunsetblow]

You know how now with the new iBooks app, iTunes is supposed to just pull the library from the app in order to sync to devices? Well, the two have been unlinked by some unknown force and now the only two things showing up in my iTunes (thru device view) is my purchased items (not my PDFs or other ebooks).

Have tried:
- Uninstalling and reinstalling iTunes
- Rebuilding iTunes library
- Reimporting all books/pdfs into iBooks

Any thoughts?