When Nautilus is running it does not group open instances with the pre-existing docked icon. It adds this file cabinet looking icon to the task bar. I know this isn't default behavior and I'm wondering what could be causing this?
I believe I started noticing this happening after I upgraded (via update manager) from 11.04 to 11.10. Not 100% sure about that though. I do have a quicklist## Heading ##
In the picture I've got my mouse on the extraneous icon.
What you should do is open your custom .desktop (nautilus-home.desktop file in ~/.local/share/applications
Inside you'll likely find a line -
Remove that line & you can again use your custom .desktop, all nautilus windows will be launched & controlled from the single "Home" icon. A log out/in may be good to do
You may also wish to return the .desktop in /usr to orig. state
A 'bug' report on, though i'm not sure the use of copied .desktops is a bug https://bugs.launchpad.net/ubuntu/+source/unity/+bug/881235