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Renaming the metadata.calibre file on the Kindle doesn't redo your kindle from scratch - it just removes the cache file that Calibre uses. By renaming it, you force calibre to read through all the books on your device to get their information so it can rebuild the cache file to save time each time your device is connected. But if the settings below aren't in sync I don't think it will help.
Check Preferences -> Adding Books - is Reading metadata from file checked or unchecked
Check Preferences -> Plugins, then expand Device Interface Plugins, then click Kindle 2/3 Device Interface, then click Customize Plugin. Is Read metadata checked or unchecked?
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