I saw few articles from the today's paper (Toyota to Cut Bonuses 10% ..., Conglomerate Bets on Macau, Chicago Banks on Private Parking) that were not in built in version. This may be related to the limit on number of articles.
I will try the built-in recipe again with more articles in each section. Now it's easy to modify it within Calibre, I can remove feeds that I'm not interested, to minimize the size of the file (it's 12Mb today).
Is your change for limit by article age in Calibre or you have it locally? Can you share it here?
Edit: Is this the option to control the age: "oldest_article = 2"?
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