I have this issue as well. Running The GM of El Capitan. Console shows several log entries like the following for different classes:
iBooks[2491]: objc[2491]: Class SFUZipException is implemented in both /Applications/iBooks.app/Contents/Frameworks/TSUtility.framework/Versions/A/TSUtility and /Applications/iBooks.app/Contents/Frameworks/IMCommonCore.framework/Versions/A/IMCommonCore. One of the two will be used. Which one is undefined.
Then a different error:
iBooks[2491]: Unsupported configuration. Please update your BookKit.framework.
The iBooks library is configured for its default location, ie. it is not a externable drive.
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update. I just noticed this is an ios9 thread. I am experiencing this problem on OSX El Capitan GM, I'll leave this here in case the console log proves helpful.