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I have two guess. Calibre is automatically sending new versions of the news source. Calibre is automatically sending the news to the device when you connect it and then you are manually sending it.
If you really only have one file for each new source (be sure to check the news, magazine and books folders in My Files for duplicates) then it sounds like there is something wrong with your Nook. There is no DB for instance with the Nook. It just reads the files that are on the device. Also check the SD card if you have one.
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