I have a Kindle as well and have noticed the same thing. My understanding is that recipe output files are marked as periodicals, which the Kindle treats differently from other ebook files. (It will show the most recent available issue on the home screen, as you note, and also prevents you from manually filing the issue in a collection.)
I don't know if there is a simpler solution, but I have found that if you use Calibre to reconvert the recipe output to MOBI (even if it is already a MOBI file), the new file will not be marked as a periodical and you can therefore manage it as you expect.
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