@Ekopalypse , @Alan-Kilborn , and others,
I think the difference is that in the situation called, there are two layers: there’s the NppExec script, which is being called by the shortcut; then the NppExec is using SendMessage to activate the PythonScript menu from a “click the menu equivalent”.
So while the shortcut is associated with the NppExec script, it’s keys are still “active” when the menu is “clicked”, so the PS check of “am I being Ctrl+Clicked” sees the Ctrl from the NppExec shortcut and the click from the NppExec SendMessage.
Whereas, when you just run a PythonScript with a keyboard shortcut, it isn’t also getting the “clicked” attribute.
At least, that’s what I’ve gathered from the evidence given in this dicsussion; I could easily be wrong.