*** This bug is a duplicate of bug 391056 ***
    https://bugs.launchpad.net/bugs/391056

I don't know what you expect the list of open windows to contain, but if
you 'close' a window to the tray it is no longer open.  Thus, this is
the correct and intended behavior and is the same behavior as the window
list in gnome-panel.

Adding a notification area docklet to Docky is bug 391056 so please
comment there.

** This bug has been marked a duplicate of bug 391056
   Implement a notification area in Docky

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window close will remove an app from docky
https://bugs.launchpad.net/bugs/422556
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