@Marcy:
In iTunes|Preferences|Advanced|Copy files to iTunes Media folder when adding to Library: checked or unchecked?
In iTunes|DEVICES|Summary|Options|Manually manage music and videos: checked or unchecked?
In iTunes|LIBRARY|Books, are the books that you've transferred from calibre listed there? Do they have a '!' in front of them?
After transferring books from calibre to iTunes, what steps are you taking to sync your iDevice with iTunes?
G
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