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I have had the same problem with front page articles, though the time frame is different. (Though not sure what timezone you're in) Always used to be able to get everything at 4:00 am (Pacific), never downloaded anything as late as 7:00. E.g. today got only one front page article at 4:00, but manually downloaded NYT at about 6:30 and got full front page.
Am now loading two copies of the recipe, one to download at 5:00 am, the second at 5:45, just to see what happens.
It's strange. The paid Amazon Kindle version of the paper appears quite early on the West Coast, at the same time it would hit the streets in New York. I don't wake up at 4:00 am, but it has certainly been there at 5:00 am (8:00 Eastern time). So those articles must be available someplace. And they were always available through calibre scheduled downdloads as early as 3:40 am (Pacific) a few months ago!
At one time I had thought that the problem had something to do with the "duplicates" variable. IOW that if any "International" article were on the Front Page of the paper, it would only appear in the "International" section, but not be repeated on the Front Page. But alas! Not so. The actual front page articles seem to be missing from the entire paper!
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