When applying themes that have transparency set on the top bar (gnome shell/gnome 3), there is a unity or nautilus bar behind it that makes everything look like a mess. That bar contains menu items like : file edit, about, help Once i did the help button, when gnome 3 didn't start properly (so i was able to access this menu), and it said "Nautilus". I've seen that ppl around the net have this problem but does anyone here have a solution?
3 Answers
This is because nautilus is handling the desktop You can disable it using gnome tweak tool if you dont have it it's
sudo apt-get install gnome-tweak-tool
to install it
Then just turn "have file manager handle desktop" off as shown here

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I had the same problem myself, and after looking around I solved it. Fire up Synaptic and remove "appmenu-gtk" and "appmenu-gtk3" Log out or reboot and the menu should be gone. You aren't using Unity so you don't need them anyways.
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It's definitely a nautilus bar. If you kill nautilus processes, it goes away, but it comes back as soon as you start a "Files" activity. I have the same thing on my machine, but it's on my secondary monitor rather than behind my Gnome 3 bar. I've no idea how to get rid of it, unfortunately. I'm guessing it's related to the unified menu deal from Unity...
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