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Calibre should work fine. Perhaps the pdf has DRM protection? If so, you cannot convert the file. You can always download Mobipocket Creator, Publisher edition from Mobipocket.com (free) and use it to convert a pdf to Mobipocket (Kindle) format. Calibre should work, but I found that initially I had to keep going back and tweaking the default output settings to get it to create Mobipocket output like I wanted.
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