For some reason sometimes when I have a nautilus window open, then switch to a different window, when I click on the nautilus icon in the Unity bar, it opens a new nautilus window instead of the existing one. Yes the old window is still there, if I minimize the fullscreen window it reveals both of them, and the nautilus icon has two ticks. I think this question's been asked already, but there's no solutions.
Sorry, after some time the problem returns.
So I trying other solution, and this time really solved!
sudo gedit /usr/share/applications/nautilus.desktop
At flag "Exec=nautilus --new-window %U" remove part "--new-window %U"
I watched a video and it says that the problem can be solved by NOT clicking on it , instead you just scroll your mouse over the Files icon . It worked for me.
In my case I solved doing this: