Maybe it needs investigating further, I have the same problem after installing
the [Windows 10 1809] March 1, 2019—KB4482887 cumulative update. It could be the February one, b/c I skipped on it at first.
I could repair the 3.39.1 current install, but after I uninstalled it, calibre won't reinstall using either the 3.39.1 or 3.40.1 MSI (x86 or x64)
I have F-Secure as antivirus, but no sign anything was blocked.
EDIT: see also
https://communities.vmware.com/thread/606337 KB4487044 for Windows 10 1809 seems to be the culprit
EDIT2: Workaround!
- Open an UAC-elevated "Command Prompt"
- Launch the MSI from there (directly entering its full path in quotes)