Example #1.) You use Firefox, download a file and then want to use the menu to "Open Containing Folder". Example #2.) You add "Files" to the e17 engage launcher. Both of these examples will still launch nautilus with the desktop.
The solution (actually quite silly): You will first need the dconf-tools (this is an editor for the dbus configuration). To install it use the Package Manager or the following command line:
$ sudo apt-get install dconf-tools
$ sudo dconf-editor