I'll check for iTunes updates and look into the work-arounds you suggest. Too many PDFs to email (something like 50-100). Thanks for all your help.
I have another problem that I think might be related (one issue causing multiple problems like iBook sync).
I did something that caused an iPad backup without me asking for it. Once complete, my iPad did not have any files on it. I have all my apps and purchased books etc, but PDFs and files associated with another program I have are all gone. I tried to restore from a previous backup and the files are gone there also! So last night's backup went fine and I had all my stuff this morning. Then this new backup happened and my files are gone, and restoring last night's backup did not bring my files back. Arrrrg!!!
I'm now restoring a backup I did on my PC 1 week ago. I noticed that iTunes does not store multiple backups either on the PC or Mac. They just keep overwriting the same file. I have gotten into the habit of copying the backup file and changing the name before I do a new backup. I don't think that worked on the Mac the way it did for me on the PC.