Try running 'calibre-debug -g' instead of calibre.
I built a task specification to run a .bat file that sets a few environment variables (because I didn't want the test to touch my real library), then runs calibre-debug -g. It runs it every 5 minutes, killing it after 1. It has been happily doing this for 20 minutes. I haven't tried running it when I am not logged in, so can't say whether not having a screen will cause the GUI difficulties.
I suspect that running calibre-debug gives the task scheduler a convenient process to kill.
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