Take a look at this wiki page,http://wiki.linuxmce.org/index.php/Howto:_Using_Network_Shares
I ran the following script from the command line and I found out that my FREENAS box was trying to be a master samba server which was causing conflicts.
sudo /usr/pluto/bin/Configure_1837.sh -d <device number>
After I corrected the FREENAS box, I then ran the above code and the Shares were no automatically set up.
It turned out to be something very simple, but nonetheless, I have been struggling with this for quite some time.