No idea why one Kindle would work fine, but not the other if they've worked fine recently on another computer. Do you still have the older machine (or access to some other computer) to verify that both work somewhere else? Are both Kindle's running the same firmware version?
FYI the black model is newer (released Sept 2012) than the Silver/Gray model (released Sept 2011).
What are the file extensions for the duplicate files? You'll often get a book file and then files with the same name, but different extension, such as .mbp and .apnx. These are files the Kindle uses internally for things like bookmarks, notes, page numbers, etc.
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