Apologies – this was a “pebcac” issue 🙂
I’ve been working with minimal content as I’m in the process of a redesign, and with the effects, there is a small amount of “dead space” between the menu going out of view and coming back into view with the effect. I had so little content on my page that the menu didn’t come back into view. Once I added a bit more “lorem ipsum” I found the issue!
