I had this same issue. I realized that I had confused the Windows built-in screen clip shortcut with the Evernote shortcut.
"Alt + Ctrl + S" is Evernote screen capture
"Windows + Shift + S" is windows clip tool
Both options effectively work the same, but the second option doesn't invoke anything in Evernote.
If you want to disable the Evernote shortcut, open Evernote, press "Ctrl + /", locate the "Capture screen", select the "..." menu and then "Disable".