Bookcase has a bug that when the same image appears in multiple entries and the collection is saved, Bookcase won’t re-open the file. The bug is that I wrote the same image to the zip file twice, but KZip has problems with that. Neither ark nor file-roller care, though; they’ll open the bookcase data file anyways. I filed KDE bug 76791 about KZip’s robustness and I fixed the Bookcase bug as well. I’ll try to get out an updated version this weekend, perhaps.
If you have data and Bookcase won’t open it, try using file-roller to open it and then resave the file. (Yes, I know it’s a GNOME app…) That fixes the problem, at least until you save it again from within Bookcase. That won’t work with ark, unfortunately, for some reason.
As always, this is mostly a guess on my part. Who knows, maybe I’m just using KZip all wrong.