The files appear to be the exact same except for line 8, which I cannot read as it contains special characters. I assume that has to be something to do with the filename though as it all seems to be header-related information up there.
But with the exception of that single line, all of the rest of the content in those 2 files are the same.
Since you said the template for these files is "title - author id.ext", it stands to reason that the files with "- calibre" in the title are the correct ones and the others are dupes caused by some sort of bug going on. I'm using calibre to transfer the files in this case. The files that calibre transfers include index numbers on the end while the local PC copy does not.
I'm sure that someone else with a Kindle 2 would be able to verify the duplicate file bug for news. I'm not doing anything out of the ordinary and am using the included recipe for Engadget and Lifehacker just used it's own simple recipe (created simply by inputting the URL and that's it).