Yes, I have suddenly starting having this issue too. I used to put epubs from Instapaper.com onto my Kobo with Calibre all the time, no problems. But the last two times I have tried I get the same problems as the original poster.
Calibre says it is on the Kobo, but the Kobo does not list it.
I have checked the filesystem on the Kobo, and the folder for the epub is there with the epub within it.
What broke?
Firmware 1.4, Calibre 0.7.20.
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