I'm Using Ubuntu 12.10, I used the standard Gnome 3 ppa to update all the GNOME apps in 12.10 to version 3.6 including Nautilus. Then I realized that It didn't update Rhythmbox to version 2.98, so I got the GNOME Shell ppa (Aka the "ricotz" testing ppa). Than I typed sudo apt-get update in the terminal, then I opened the Software Updater and no new packages were found. So I edit my sources list so that it would get the Precise testing packages. I ran sudo apt-get update opened Software Updater and installed all the updates. After this I went to change the ppa's file to get quantal packages and so I used sudo Nautilus (Note that this was AFTER all the packages were installed and system was restarted) and I got the 3.6 version. After I wanted to see a document so I opened Nautilus from the menu in GNOME Fallback and I was surprised that I got the 3.4 version! So then I went in the terminal and typed "sudo nautilus" and the 3.6 version showed up! So I had both the 3.4 and the 3.6 version on my screen!
So what I want to do is not remove the 3.4 version, but add an icon to the GNOME Fallback menu (Preferably under accesories) that will launch the 3.6 version as the 3.4 version does some things better and the 3.6 version does somethings better. (Note that the 3.4 version uses the nautilus %U command)
I was told to run some commands in the terminal and here is what I got david@david-VirtualBox:~$ nautilus --version GNOME nautilus 3.6.3 david@david-VirtualBox:~$ dpkg -l | grep nautilus rc libnautilus-extension1 1:3.2.0-0ubuntu5 amd64 libraries for nautilus components - runtime version ii libnautilus-extension1a 1:3.6.3-0ubuntu6~ubuntu12.10.1 amd64 libraries for nautilus components - runtime version ii nautilus 1:3.6.3-0ubuntu6~ubuntu12.10.1 amd64 file manager and graphical shell for GNOME ii nautilus-data 1:3.6.3-0ubuntu6~ubuntu12.10.1 all data files for nautilus ii nautilus-sendto 3.6.0-0ubuntu1 amd64 integrates Evolution and Pidgin into the Nautilus file manager ii nautilus-sendto-empathy 220.127.116.11-0ubuntu1 amd64 GNOME multi-protocol chat and call client (nautilus-sendto plugin) ii nautilus-share 0.7.3-1ubuntu3 amd64 Nautilus extension to share folder using Samba david@david-VirtualBox:~$
It looks like the 3.4.2 version on the system is a bug.
Here are some images: