Calibre is set to download the paper after 6:00am. The Mac goes to sleep after 3 hours so if I head to the land of nod at 11pm, it will sleep around 2am.
I went away for 2 weeks & left the Mac on & the papers were still emailed & they were complete on most days.
It seems that when I wake the Mac, it seems to only download a few hundred KB of the file.
I'm convinced it's OS X but looking at my sent emails, the ones that are being emailed when I wake the mac are more likely to fail!