I have similar problem - i have 10.4 version, which is supposed not to have many shortcuts known from previous version. Unfortunately, it has. An example - shortcut alt-s, which in my county is dedicated to one of local signs, still work in my 10.4 fresh installation as print screen capture (there was no evernote on this host before). In previous version (on other computer) i could disable this shortcut. In 10.4 version, I can do nothing with this. Please, restore Tools --> Options --> Shortcuts immediately. I have no access to this using 10.4 version of Evernote for Windows 10.