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 :)
We have a lead on a fix for it but it will take some development time before we'll know if it will work or not, so we can't guarantee a timeline on when it will be implemented.
Thanks!