I had the same problem with fresh install of 17.10 when opening a new window of Nautilus using CTRL+N shortcut. I avoid that message creating an additional shortcut for Nautilus:
- Go to keyboard settings, you should see the list of keyboard shortcuts.
- Click on the "+" button at the bottom of that list to create a new shortcut.
Create a new shortcut filling the params asked:
Name = Open nautilus (or any other name you want)
Command = nautilus (like when you open nautilus from terminal)
Shortcut = Press the "Set Shortcut..." button and press **CTRL+M** (or any other combination you want).
After setting the new shortcut for CTRL+M, close keyboard settings and the new shortcut will open nautilus without the "x-nautilus-desktop:///" error pointing to your home folder.
Hope this helps.
EDIT (WARNING): The solution described helps to avoid the error mentioned, but not to solve the error itself. If you try to overwrite the CTRL+N shortcut that will overwrite the shortcut for any other app. That is, for example, after CTRL+N overwriting in Google Chrome will open a new Nautilus window and not a new Chrome window. In my case, I set new Nautilus window to CTRL+M. This does not solve the "x-nautilus-desktop:///" error itself, but it's an alternative solution. If you set a new shortcut for Nautilus new window as CTRL+M, if you use CTRL+N you still get the error mentioned.
You can set the command param for opening nautilus in any directory you want, for example:
Command = nautilus ~/Downloads will open nautilus in Downloads directory when CTRL+M is shortcut is used.