Apple recently updated iBooks. It’s just a fix that improves compatibility between iOS and iCloud.
It’s not said what exactly the fix is, but according to website TUAW, it seems that it’s intended to fix an ongoing problem in which bookmarks didn’t properly sync across devices. Maybe this will correct that. As the report says, this is especially important right now, because Apple is releasing iBooks for OS X soon. It would be ideal if things synced across all platforms properly.
iBooks is available on the App Store.