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I've had this same problem, except when calibre was trying to email a document to my device. I even got the requisite 4 popups I had to click through. The problem in my situation was that I had incorrectly set up the smtp settings, so that portion of the job was getting stuck (it kept retrying it at longer and longer intervals I believe). Is this a bug that is being worked on, because I felt somewhat frustrated that I couldn't actually kill a job when I wanted to. I found myself doing a ps aux | grep calibre to see if maybe (by chance) it had branched the smtp job into a child process. Anywho, aside from this great program, it really is a treat to use.
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