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OK, I did some testing; I modified some options in SP, then deleted all the books in the library with Master Controller and let the game regenerate them. It appears the issue was with NPCs writing books; there were about 1500 regular books, and a whopping 5000 written by Sims - which, unfortunately, were titled the same as the books programmed by EA. This explains why two copies of "Special Snowflake" had the generic book cover instead of the red one reserved for romance novels.
These are the settings I used for SP (all under General \ Lots):
Automatic Cleaning: set it to anything other than 0
Cleanup Duplicate Library Books: False
Remove Zero Value Books: False
Repopulate Empty Library Shelves: True
And under General \ Skills, I disabled Push Writing. I don't really care about inactives writing books.
Edit: oh, and I also disabled "Add Written Books to Library", under General \ Skills.
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