I've the same problem and followed it up with Apple Support. They tried various things but came back to me and said they were replicating the problem on their equipment too so classed it as a bug to be solved (perhaps) in a future (but unspecified) update.
However, I switched back to iPhoto which is still in Applications folder and suddenly iBooks Author could see the photos in the old iPhoto. So for now I can work the way I did by going back to iPhoto.
One caveat..... You can either use iPhoto or the new Photo but I don't think both. So I think if you use iPhoto for writing ebooks, it may not show new photos imported into the new program.
Hone this helps until Apple, fix what they broke!