I had exactly the same problem and quickly wanted to share my amateurish "solution" here.
The issue: nautilus would not open any folder located on desktop by doubleclicking or by right-click and "open". (Browsing through the filemanager and opening the desktop folders from there worked fine - just as everything else concerned nautilus).
What I did:
For the sake of completeness I want to mention that I started with a lot of uninstalling, purging, reinstalling, apt-getting etc. of nautilus. Being rather a beginner than an expert I can't assess properly whether this step was necessary at all, but if you want to do it:
sudo apt-get purge nautilus
sudo apt-get install nautilus
As mentioned, this didn't change a thing, but here comes my breakthrough attempt: I reinstalled the gnome-shell:
sudo apt-get install --reinstall gnome-shell
(I somewhat suspected / guessed that something else apart from nautilus messed with my desktop folders and kept it from acting in a well-behaved manner).
That's it. Maybe this works for you or at least gives you a hint to check your system for stuff that interacts with your desktop and isn't set up neatly.