Your script has a bug - a URI is not the same as a directory. cd file:///home/user/Desktop is not the same as: cd /home/user/Desktop "cd" is an old skool program that knows not of URIs. Use some sed in there and it'll work:
#!/bin/bash gnome-terminal --working-directory=$(echo $NAUTILUS_SCRIPT_CURRENT_URI | sed 's!file://!!g') -- NAUTILUS_SCRIPT_CURRENT_URI is set to $HOME when executing scripts from desktop https://launchpad.net/bugs/49767 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs
