Sorry had to travel off on business. I'll try to answer the questions as far as I understand them.
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This is a new problem that suddenly occured, did it use to work (with other libraries, etc etc ) ?
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I'm not sure if this just started happening. My original library is about 8000 books and until I created the new empty library I may not have noticed if all the books didn't show as being on the device. I'd just added the collections plugin and my purpose in creating the new library was to have a place to work with just the books on the device and their collections, so of course I noticed it then

Before this point I was doing collections by hand.
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Which Kindle do you have ?
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Kindle 3 3G
3.1
Windows Vista Ultimate
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Mobi books on Kindle: Are they DRM'ed ? (copy protected) ? Your azw and azw1 DRM'ed ?
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Half and half. The azw/azw1 probably about 75% copy protected, the mobi stuff is not.
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What's the size of you metadata.calibre on Kindle ?
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4,131 KB
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Are ALL books on your Kindle transferred via Calibre ?!!
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no. The amazon azw/azw1 stuff downloads from Amazon. The mobi stuff is sideloaded via USB from the main Calibre library. I imported them all from the Kindle (USB) to the Calibre empty library in order to do collections on them.