If I remember correctly, at that stage of the installation, the installer generates checksums of every file in the Calibre install directory and compares those with the checksums of the files it wants to install. I've heard that this has to be done because Calibre is written in Python, and the associated files cannot store the checksums needed, unlike "normal" .exe and .dll files. It might be that Kaspersky gets confused by the huge amount of disk access performed during that phase. You could try to exclude the Calibre install directory from the real-time search.
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