Ha a , yea, I did in fact check the obvious, but also in the mean time I have fixed it. I had to remove them from the itunes library, and then discovered that for some reason, they were renamed to have two .PDF extensions, and it was this it seems to have been causing the issue as iTunes could not locate them.
Once renamed to remove the excess .PDF and re-added to the library, then ticked they then synced!
Others might be interested in this design feature of iBooks and iTunes