Adam, that's because you blacklisted that device icon from staying
pinned to the launcher.

But as it was an un-pinned app, once you open it it has to stay to the 
launcher. The same behavior would apply to an app that you open and close.
I don't think that grouping it with nautilus is the right solution in that 
case... It would probably easy to do it (patches with optional settings 
welcome, and I can help you guys to go through the codebase), but I don't see 
this as being coherent.

As general consideration, I think the simple association is:

The fact that nautilus can have a tabbed view makes things harder. I actually 
supported tabs in my initial implementation, but there was the problem where a 
window was matched by multiple icons, and I think this was wrong (what to do if 
you had multiple locations opened, from the same devices, spread around 
multiple windows and tabs, when activating the "app/device" window 
spread/scale?).
So the thing was just simplify it by considering only the main (active) view of 
a nautilus window.

The fact that there are multiple launcher icons for different device
locations, it's just as it has to be. We didn't want to patch nautilus
aggressively in order to be more "locked" in this scenario, thus there
could be some odd behaviors, but I think all this allows to manage
things quite well for the average user.

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https://bugs.launchpad.net/bugs/1170647

Title:
  After minimizing a Nautilus window of another partition or external
  media or Trash folder, clicking on the "Files" icon on the Launcher
  again doesn't restore the minimized window, but opens a new one

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