The menu is set in Appearance -> Menus. It is the only menu and is also set as the primary.
I’m not sure what else to do? The menu is not recognizing clicks at all. I used console.log to log the clicks in the small-menu.js file, and it doesn’t recognize the clicks. I have also tried adjusting the z-index, as another user in the forum had, but that didn’t work either.
I would revert to the previous version of Jetpack, except that the Twitter widget stopped updating…