Thanks for that video example Trent.
Mine works correctly in simple situations like that, as well. But real-world edits are a mess. So I need to correct my description. Turning Layered editing on and off does make a difference. But Shuffle mode gets messed up by layers whether it's on or off. This does change the nature of my pending Ideascale post. Instead of reporting it as a bug, I will request that Shuffle mode editing work the way it did before layers were a thing.
May I ask what you used for video screen capture?