This problem happened on Ubuntu using Gnome shell and the gnome3 ppa [1].

I was going to report this on the gnome3-team page, but it doesn't seem to accept new bug reports (I can't find the "File bug" link/button). And it's not a problem with Ubuntu's package of nautilus since it's from gnome3 ppa.

The problem happens when trying to run nautilus while it's handling the desktop (by handling, I mean showing folders/files/etc). To reproduce:
1- Like I said, be running Ubuntu 12.10 with Gnome shell and using the gnome3 ppa.
2- On gnome-tweak-tool, set nautilus to handle the desktop
3- Try to run nautilus from shell (searching for 'Files' for example) or from a terminal. The problem happens. (note that it doesn't crash when opening it by double-clicking a folder in the desktop).

If I uncheck that handling desktop option the problem doesn't happen anymore.

[1] https://launchpad.net/~gnome3-team/+archive/gnome3