This has only happened occasionally, and it might be something to do more with Calibre itself perhaps, but when I go to update fanfics and the process is on the 'Downloading metadata for stories' window, sometimes the process will stop and disappear when I go an load other windows.
I think it might be happening because I have set Calibre to be appear as an icon next to my clock. I noticed that the plugin will sometimes freeze and flash away and back between each story for metadata downloading. So maybe during that brief window, Calibre decides it can go in the background?
It's not a big thing, has only happened about 2 or 3 times now. And it seems to occur most during the beginning of the download process.