Hi All,
One last attempt at explaining how this is still working for me, with a clarification on my 9 Dec post: All books works better than Selected Books.
1. Open iBooks on your Mac, go to Preferences, then in General make sure check box next to Sync is ticked
2. Select Collections from top menu in iBooks, then select PDFs from the side bar, and drag your new pdf into the main window (of PDFs). If you drag it to another collection it goes to PDFs anyway. You may move it to you chosen collection then.
3. Open settings on you iPad and swipe to iBooks on the sidebar. I have both Sync Bookmarks and Sync Collections slider buttons on (green colour visible).
Also check at the top of the main window if it says IBOOKS 3.2 (2038). Perhaps if you have an older version installed on your iPad, you could go to iTunes & App Store setting & select AUTOMATIC DOWNLOADS for Apps, or open App Store, select Updates on the bottom right & manually update iBooks.
4. Close iBooks & open iTunes. Plug in your iPad and immediately stop it from syncing (if it is set to do this automatically). Then click the iPad button, showing the menu items: Summary, Apps, etc. Click on Books. With the sub menu Books and PDF files selected under Books, tick the box Sync Books and Select the button All books.

5. Click Apply (bottom right), then click Sync (same position). Hopefully your new pdf will appear in your chosen collection in iBooks on the iPad!