the version currently available via the VS-gallery loads all the commands once and saves them. It loads them from the file when you start it again. This can cause trouble when you change something or install another extension afterwards.
On GitHub (https://github.com/PapaMufflon/CodeNinjaSpy) is the newest development-version (you'll need VS-SDK to compile it) which should work correctly.
If not, it would be awesome if you could activate debugging (s.f. https://github.com/PapaMufflon/CodeNinjaSpy/issues/1#issuecomment-2460792).
An interesting twist would be the other way round: if you invoke a command (from the menus or toolbars), show the corresponding shortcut, if there is one. I think that would help a lot of people tremendously to transition from mouse to keyboard ninjas :).
Works like a charm, also with other add-ins like ReSharper! I had to remove a "Ctrl-#" shortcut that focused the search combobox, because apparently this gets invoked a lot automatically (didn't use it anyway). Two things I've noticed: 1.) For example I use Ctrl+E, Ctrl+D for Edit.FormatDocument, but Code Ninja Spy reports Ctrl+K, Ctrl+D. That made me realize that some commands have two or even three shortcuts applied to them (don't ask me why, I didn't consciously do that). Maybe Code Ninja Spy could show all of them? 2.) The extension does not update it's database when you change shortcuts in the options. That requires a restart of VS. But I don't think it's a big issue, I can very well live with that, and you don't change these shortcuts frequently, do you?
Thanks again for adding this in, this will actually make me use it actively to learn even more keyboard shortcuts :).