I've had the same problem and upon looking into it, it's because for some idiotic reason it's designed that way. If you look at the tuning for a book, storage boxes are a valid inventory type, right alongside the bookshelf and a sim's inventory (and a few sales spots). And the worst part is, as far as I can tell, to change it, you'd have to go into EACH and every book type; there isn't one object called book. And you can't do it on the storage boxes end; they don't say what goes in them, the objects say where they can be put. So I doubt this will ever be fixed; simple fix but it would take forever to do it.
This still happens with every chest I've tried but also with the Eco sticker boxes. Also tried placing bookshelves next to boxes, but they still prefer the box. I like to use the boxes as decoration, but it's too much of a hazzle with this bug.
Just want to add that this also makes the books disappear from the bookshelf index, so there's no way to make sims read the books unless you know where they've ended up.
I am having same issue since December update. Windows 10 PC. Have never used mods or CC.
