I had a bit of a lengthy session first w/ Apple-IOS support and then, at her suggestion, with Mac Support. The end result is that this is indeed a known issue and the tech hopes that it will be dealt with soon. He has had 3 recent reports of the same thing and suggested that I send a note to apple.com/feedback to insure that the techs see it. I sent the below note, and suggest y'all do the same.
In the meantime, the work-around solution is to get a 3rd party app, like Adobe Acrobat, and use iTunes as a conduit to move the PDFs onto your iPad, etc.
Once you've installed the App from the App store, when the iPad is connected, go to the Apps Tab and click on the 3rd party app. In the box next to it you have the option to Add documents to the App, or you can click and drag them into the box. Voila!! PDFs on the Pad!
This is what I sent to the feedback page:
W/the changes to iTunes re: moving books & PDF's to iBooks & being entirely removed from iTunes, it's become impossible to manually move PDFs from my macbook to a shared iPad or my iPhone. I can still click & drag all of my tunes and videos to it, but no longer can I simply move PDFs. I know there are licensing issues w/book publishers, but I'm a student & get many PDFs as handouts from instructors. I like to put them onto my family's shared iPad & read while commuting. I can still do the old way of emailing them, but not when the file exceeds 25mg. Your tech gave me the work-around of using a 3rd Party app, like Adobe Acrobat, & using iTunes to add it to the app. That indeed worked, but now I have PDFs in 2 locations. What happened to Apple Simplicity? Please bring PDFs back into iTunes..