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I am not sure why all of this is being raised again. Perhaps a summary of what I think we learned back in posts 130-170, ignoring the bonjour bits, is in order.
At some point after a boot Windows will verify that its program files are consistent with what should be there, where "should" is determined by the windows update files. As far as I can tell, almost any program can trigger this check. Once it is triggered it runs to completion. Windows is doing this check for security reasons. It is trying to detect if some malware has made it onto the system since the last boot. If it detects inconsistencies it (I think) replaces the broken program file with a correct copy. The time it takes is proportional to the number of updates stored on the computer. Reducing that number to the minimum using the disk cleaner and a reboot is the best one can do.
Calibre has the bad luck of being a trigger. As far as I can tell, there is zero that calibre can do about it.
On my system some other program triggers the scan during the boot cycle. I am not sure which one, but by the time my system has stabilized after a boot (multiple minutes) the scan has been done.
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