I know this is an old thread but I recently had this same issue, except the other way around.
I had a few boards that I had been invited to on web. Eventually decided to get the macOS desktop app, and when I logged in, only the boards I had made were visible to me. It was not at all intuitive for me to access boards shared with me from the app. In the end, I had to manually open all of the boards shared with me in my browser, whereupon I was prompted to load them in the app.
Not the end of the world, but it would be a lot better if they auto-populated. If I had a ton of boards this would have been a real pain.