I think it's the same issue I have in some projects I created from a project template that I created during the X3d period. I've tried to reproduce it in a new project created from the Normal project template, only to fail. My issue is that MIDI clips often don't link in Take lanes, and also clips in tracks don't link when duplicated together with clips in expanded Take lanes. I have the "Copy Entire Clips as Linked Clips" option in Preferences always enabled.