[KevinH]

Again unlike calibre, no plugin is run on Sigil start-up and in fact none are run until something is actually launched by the user in Sigil. Only a list of the folder names and parsing of plugin.xml files is done, and None of which can prevent shortcuts from being delivered to Sigil itself. So you can safely ignore the plugin directory. Might try with a different ini file just to rule that out.

If this was a linux box or macOS, I would bet ownership or permissions of Sigil itself or one of its components is messed up requiring Admin privs to connect to it. Or alternatively the HotKeys stuff is being run under some other owner or permissions and therefore without admin privs can not deliver events to Sigil.

Or some other piece of software is launching Sigil under its watch (and its ownership or permissions). This may be caused by some strange system monitoring tool or anti-virus tool.

Or If AutoHotKeys is being run as a service (or server) my guess would be it is being launched or run with the wrong permissions or ownership.

I would examine the Windows property setting for launching Sigil. Check or update ownership of all of Sigil and its components.

Then try directly launching Sigil using a commandshell or bat file.

Or create a new user and install Sigil using the official installer under that new user to see if it exhibits the same strange symptoms.

Either way, this issue is specific to his/her machine in some way.