@jackr - I've never tried the system tray feature of calibre before.
I bet that you tried to minimize calibre to the system tray.
If I click the calibre system tray icon to hide calibre while it's downloading metadata, it aborts the plugin as if I'd clicked the close button on the progress bar.
I see the same behavior from Generate Cover, so I expect any in-progress action that can be cancelled, will be. Copying from one library to another doesn't get cancelled, but neither does it cancel when you click it's close button.
So I'm going to call it a general calibre behavior. I think being able to abort the download is more important than hiding to system tray.