Comment 5 for bug 511511

I've tried both of the methods suggested here and as was mentioned with the first one you get the negative side effect. The second one didn't work for me unless I added the period but that gave the side effect still. I found a way that has worked on multiple machines with no side effect:

1.) In the terminal: sudo gedit /usr/share/applications/nautilus-browser.desktop
2.) Change the following lines and then save and close the file:

a.) "Exec=nautilus --no-desktop --browser %U" should be changed to "Exec=nautilus --browser ." (You can probably leave in --no-desktop if you want, I tried it with and without it).
b.) "NoDisplay=true" should be changed to "NoDisplay"=false

3.) Navigate to /usr/share/applications and find the File Browser (not the File Manager). Drag and drop the File Browser into Docky and it should start working right away!

As I said, I've tried this on several different machines and it seems to work on each one without any troubles or side effects. If you have issues post again and let me know.