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This issue is currently on our list to fix up. For some reason, windows that have been removed from the Primary taskbar (like ones that have been moved to a DF taskbar) don't register in Task View any more.
There is a workaround, which is to set the Taskbar Mode on the Settings > Taskbar tab to "Windows taskbar shows all windows..." It's definitely not ideal, but hopefully a decent compromise until we can find a way to fix it up in the future
