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Maybe asking my question in this way was incorrect. when I switch into Gnome session and use a theme that have a transparent dock, in top left of screen there is global-menu for nautilus.

I edited one custom theme and change #panel height to a short height, I can use global-menu.

maybe it's a simple bug in 11.10 beta2 release, but how can I remove this?

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This is a known bug in Nautilus. Currently there is no known fix other than to disable Nautilus drawing the desktop:

The temporary solution I have found it's to disable the 'Have the filemanager handle the desktop' option. You can use gnome-tweak-tool to do that. The downside is that the desktop icons won't show anymore.

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  • thanks, I didn't store anything on my desktop =)
    – Behzadsh
    Oct 13 '11 at 21:08
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you can also solve the bug and still have shortcuts on you desktop by removing global menu with

sudo apt-get remove appmenu-gtk3 appmenu-gtk appmenu-qt

This however will also have the same effect on your unity session.

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